{"$update": {"344": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "345": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "346": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "347": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "340": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "341": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "342": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "343": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "348": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "349": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1653": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2317": {"$update": {"model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2310": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "298": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "299": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "296": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "297": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "294": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "295": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "292": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "293": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "290": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "291": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "270": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "271": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "272": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "273": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "274": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "275": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "276": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}, "model_type_id": "41091"}}, "277": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "278": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "279": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1132": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2262": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2260": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2261": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2267": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2264": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2265": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2445": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "108": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "109": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "102": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "103": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "100": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "101": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "106": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "107": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "104": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "105": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2046": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2047": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2044": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2045": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2042": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2043": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2040": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2041": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2048": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2049": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1213": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2038": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1210": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2688": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2689": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4128": {"dna_sequence": {"fmax": "500039", "fmin": "497113", "accession": "NZ_CP009828.1", "strand": "+", "sequence": "AGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCTTTGGGGAGCTGTAAGTAAGCTTTGATCCAGAGATTTCCGAATGGGGAAACCCAGCATGAGTTATGTCATGTTATCGATATGTGAATACATAGCATATCAGAAGGCACACCCGGAGAACTGAAACATCTTAGTACCCGGAGGAAGAGAAAGAAAATTCGATTCCCTTAGTAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCTTGCTTGTTGGGGTTGTAGGACACTCTATACGGAGTTACAAAGGACGACATTAGACGAATCATCTGGAAAGATGAATCAAAGAAGGTAATAATCCTGTAGTCGAAAATGTTGTCTCTCTTGAGTGGATCCTGAGTACGACGGAGCACGTGAAATTCCGTCGGAATCTGGGAGGACCATCTCCTAAGGCTAAATACTCTCTAGTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGAAGGGGAGTGAAATAGAACCTGAAACCGTGTGCTTACAAGTAGTCAGAGCCCGTTAATGGGTGATGGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATTTGATGCAAGGTTAAGCAGTAAATGTGGAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGTTTAGTATTTGGTCGTAGACCCGAAACCAGGTGATCTACCCTTGGTCAGGTTGAAGTTCAGGTAACACTGAATGGAGGACCGAACCGACTTACGTTGAAAAGTGAGCGGATGAACTGAGGGTAGCGGAGAAATTCCAATCGAACCTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCCTCAAGTGATGATTATTGGAGGTAGAGCACTGTTTGGACGAGGGGCCCCTCTCGGGTTACCGAATTCAGACAAACTCCGAATGCCAATTAATTTAACTTGGGAGTCAGAACATGGGTGATAAGGTCCGTGTTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCCCAAAATATATGTTAAGTGGAAAAGGATGTGGCGTTGCCCAGACAACTAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAGTGCGTAATAGCTCACTAGTCGAGTGACACTGCGCCGAAAATGTACCGGGGCTAAACATATTACCGAAGCTGTGGATTGTCCTTTGGACAATGGTAGGAGAGCGTTCTAAGGGCGTTGAAGCATGATCGTAAGGACATGTGGAGCGCTTAGAAGTGAGAATGCCGGTGTGAGTAGCGAAAGACGGGTGAGAATCCCGTCCACCGATTGACTAAGGTTTCCAGAGGAAGGCTCGTCCGCTCTGGGTTAGTCGGGTCCTAAGCTGAGGCCGACAGGCGTAGGCGATGGATAACAGGTTGATATTCCTGTACCACCTATAATCGTTTTAATCGATGGGGGGACGCAGTAGGATAGGCGAAGCGTGCGATTGGATTGCACGTCTAAGCAGTAAGGCTGAGTATTAGGCAAATCCGGTACTCGTTAAGGCTGAGCTGTGATGGGGAGAAGACATTGTGTCTTCGAGTCGTTGATTTCACACTGCCGAGAAAAGCCTCTAGATAGAAAATAGGTGCCCGTACCGCAAACCGACACAGGTAGTCAAGATGAGAATTCTAAGGTGAGCGAGCGAACTCTCGTTAAGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTTTAGGGTTAACGCCCAGAAGAGCCGCAGTGAATAGGCCCAAGCGACTGTTTATCAAAAACACAGGTCTCTGCTAAACCGTAAGGTGATGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGGTTAGCTTCTGCGAAGCTACGAATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATCATAGTACCTGTGAAGATGCAGGTTACCCGCGACAGGACGGAAAGACCCCGTGGAGCTTTACTGTAGCCTGATATTGAAATTCGGCACAGCTTGTACAGGATAGGTAGGAGCCTTTGAAACGTGAGCGCTAGCTTACGTGGAGGCGCTGGTGGGATACTACCCTAGCTGTGTTGGCTTTCTAACCCGCACCACTTATCGTGGTGGGAGACAGTGTCAGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCTCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCATAGAGTGTAAAGGCATAAGGGAGCTTGACTGCGAGACCTACAAGTCGAGCAGGGTCGAAAGACGGACTTAGTGATCCGGTGGTTCCGCATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCCGGGGATAACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGTGGGCGTAGGAAATTTGAGAGGAGCTGTCCTTAGTACGAGAGGACCGGGATGGACATACCTCTGGTGTACCAGTTGTCGTGCCAACGGCATAGCTGGGTAGCTATGTGTGGACGGGATAAGTGCTGAAAGCATCTAAGCATGAAGCCCCCCTCAAGATGAGATTTCCCAACTTCGGTTATAAGATCCCTCAAAGATGATGAGGTTAATAGGTTCGAGGTGGAAGCATGGTGACATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus aureus", "NCBI_taxonomy_id": "1280", "NCBI_taxonomy_cvterm_id": "35508"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "5000", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2685": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2686": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2680": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2681": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2682": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2683": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "99": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "98": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "91": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "90": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "93": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "92": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "95": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "94": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "97": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "96": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1623": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1622": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1621": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1620": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1627": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1626": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1625": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1624": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1999": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1998": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "_comment": {"$update": {"description": "This file contains the complete data for all of CARD's AMR detection models, including reference sequences, SNP mapping data, model parameters, and ARO classification."}}, "1628": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "559": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "558": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "555": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "554": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "557": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "556": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "551": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "550": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "553": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "552": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1439": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1199": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1198": {"$update": {"ARO_description": "mef(B) is a macrolide efflux gene located in the vicinity of sul3 in Escherichia coli. There is also a mefB found in Streptococcus agalactiae that confers resistance to macrolides.", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_name": "mef(B)", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1191": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1190": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1193": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1192": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1195": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1194": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1197": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1196": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1759": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1758": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1757": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1756": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1755": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1754": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1753": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1752": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1751": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1750": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1177": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1176": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}, "40394": {"$update": {"param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense SNPs truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense SNPs may be attached to models, and are recorded in the format: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1175": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1174": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1173": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1172": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1171": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1170": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1179": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1178": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "511": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "510": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1005": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}, "model_type_id": "41091"}}, "1285": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1284": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1287": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "512": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1281": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1280": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1283": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1282": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1003": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1289": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1288": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "514": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1579": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1578": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "689": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "688": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "685": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "684": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "687": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "686": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "681": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "680": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "683": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "682": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1227": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1226": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1240": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "621": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "873": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1224": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "627": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1222": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1221": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "624": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2743": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "407": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1370": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "405": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1372": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1375": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1374": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1377": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "400": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1379": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1378": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1342": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "409": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "408": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "453": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2747": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_value": {"7771": "520,1445,1437,826,1248"}, "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "454": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2746": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"blastp_bit_score": {"param_value": "2661,1427,826,1337,986,152,2764", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}}, "1345": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2749": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1346": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1347": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1245": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "379": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "378": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "371": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "370": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "373": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "372": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "375": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "374": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "377": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "376": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "393": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "392": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "391": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "390": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "397": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "396": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "395": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "394": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "399": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "398": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1247": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2306": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "244": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "247": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "246": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "241": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "240": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "243": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "242": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "249": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "248": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2274": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2277": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2279": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$insert": {"40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2278": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2154": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "179": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "178": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "177": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "176": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "175": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "174": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "173": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "172": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "171": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "170": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2051": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2050": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2053": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2052": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2055": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2054": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2057": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2056": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2059": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2058": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1500": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1501": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1506": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1507": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1504": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1977": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2698": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2697": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2695": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2694": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2693": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1975": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2691": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1974": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1973": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1972": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1971": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1970": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1968": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1969": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1618": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1619": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1616": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1617": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1614": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1615": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1960": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1613": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1610": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1611": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1768": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1769": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1762": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1763": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1760": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1761": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1766": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1767": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1764": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1765": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1142": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1143": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1140": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1141": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1146": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1147": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1144": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1145": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1148": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1149": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "690": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "692": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "693": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1544": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "691": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "696": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "697": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "694": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "695": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "698": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "699": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1548": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1549": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "542": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "543": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "540": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "541": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "546": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "547": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "544": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "545": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "548": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "549": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1782": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1783": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1784": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1785": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1786": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1787": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "414": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "415": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "416": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "417": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "410": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "411": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "412": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "413": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1384": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1385": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1386": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1387": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1380": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "419": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1382": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1383": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "368": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "369": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "366": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "367": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "364": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "365": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "362": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "363": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "360": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "361": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "380": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "381": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "382": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "383": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "384": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "385": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "386": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "387": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "388": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "389": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2191": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "258": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2193": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2194": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2195": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2196": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "2198": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "253": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "251": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "256": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "257": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "254": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "255": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2200": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2201": {"$update": {"model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2202": {"$update": {"model_type": "protein domain meta-model", "model_description": "A meta-model used to detect specific domains of proteins that confer resistance to antibiotic(s) relative to wild type. These models include reference sequences, a curated BLASTP cut-off for each of the genes, and directionality of the fused genes (if known)."}}, "2203": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2204": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2205": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2206": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2207": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2208": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2428": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2429": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2400": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2421": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2422": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2423": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2424": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1849": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40394": {"$update": {"param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense SNPs truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense SNPs may be attached to models, and are recorded in the format: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2426": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2427": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2432": {"$update": {"ARO_description": "Klebsiella pneumoniae outer membrane porin protein. In beta-lactam-resistant Klebsiella, this porin is often deleted, limiting diffusion of the antibiotic into the cell. Klebsiella strains expressing OmpK35 are often beta-lactam sensitive even in the presence of beta-lactamases because of an inefficient mechanism.", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_name": "Klebsiella pneumoniae OmpK35", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}, "model_name": "Klebsiella pneumoniae OmpK35"}}, "1848": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "168": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "169": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "164": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "165": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "166": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "167": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "160": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "161": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "162": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "163": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2518": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2519": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1980": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2517": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1841": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2734": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1840": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2731": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2732": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2733": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "678": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "679": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1814": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1815": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1816": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1817": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1810": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1811": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1812": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1813": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1818": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1819": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "670": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "671": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1609": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1608": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1979": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1978": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1601": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1976": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1603": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1602": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1605": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1604": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1607": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1606": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "809": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "808": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "803": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "802": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "801": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "800": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "807": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "806": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "805": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "804": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1775": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1774": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1777": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1776": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1771": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1770": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1773": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1772": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1779": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1778": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1159": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1158": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1155": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1154": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1157": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1156": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1151": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1150": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1153": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1152": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1555": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1554": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1551": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1550": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1553": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1552": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "59": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "58": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1557": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1556": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "55": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "54": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "57": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "56": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "51": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "50": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "53": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "52": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "537": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "536": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "535": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "534": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "533": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "532": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "531": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "530": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "539": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "538": {"$update": {"ARO_accession": "3004108", "ARO_name": "Enterobacter cloacae rob", "ARO_description": "rob is a positive regulator for the acrAB efflux genes, and is structurally similar to SoxS and MarA.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "350", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}, "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41229", "model_name": "Enterobacter cloacae rob"}}, "1558": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$insert": {"40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "429": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "428": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1399": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1398": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1397": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "420": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "423": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "422": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "425": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1392": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "427": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1390": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2183": {"$update": {"model_type": "gene cluster meta-model"}}, "2182": {"$update": {"model_type": "gene cluster meta-model"}}, "2181": {"$update": {"model_type": "gene cluster meta-model"}}, "2180": {"$update": {"model_type": "gene cluster meta-model"}}, "2186": {"$update": {"model_type": "gene cluster meta-model"}}, "229": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "228": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "227": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "226": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "225": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "224": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "223": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "222": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "221": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "220": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2213": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2212": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2211": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2217": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2216": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2215": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2219": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "151": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "150": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "153": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "152": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "155": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "154": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "157": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "156": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "159": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "158": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2431": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2430": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2436": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2435": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2434": {"$update": {"ARO_description": "Klebsiella pneumoniae outer membrane porin protein. In beta-lactam-resistant Klebsiella, this porin is often deleted, limiting diffusion of the antibiotic into the cell. Klebsiella strains expressing OmpK36 are often beta-lactam sensitive even in the presence of beta-lactamases because of an inefficient mechanism.", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_name": "Klebsiella pneumoniae OmpK36", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}, "model_name": "Klebsiella pneumoniae OmpK36"}}, "2724": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2720": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2729": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "1807": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1806": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1805": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1804": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1803": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1802": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1801": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1800": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1809": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1808": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1524": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1948": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1949": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1525": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1942": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1943": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1940": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1941": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1946": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1947": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1944": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1945": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "818": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "819": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1527": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "810": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "811": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "812": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "813": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "814": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "815": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "816": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "817": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1991": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1522": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1990": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1523": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1993": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1490": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "421": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1492": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1493": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1494": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1495": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1496": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1497": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1498": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1499": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1395": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "1994": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1700": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1701": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1702": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1703": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1704": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1705": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1706": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1707": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1708": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1709": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1996": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "424": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1391": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "426": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1629": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1128": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1129": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1120": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1121": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1122": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1123": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1124": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1125": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1126": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1127": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "524": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "525": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "526": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "527": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1018": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "521": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "522": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["99", "103", "100", "97"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "523": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1014": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1015": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1016": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1017": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "528": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "529": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1012": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1013": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1234": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1235": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1236": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1237": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}, "40394": {"$update": {"param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense SNPs truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense SNPs may be attached to models, and are recorded in the format: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1230": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1231": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1232": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1233": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1238": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1239": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "_version": "1.1.9", "438": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "439": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "436": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "437": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "434": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "435": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "432": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "433": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "430": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "431": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"40394": {"$update": {"param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense SNPs truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense SNPs may be attached to models, and are recorded in the format: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1967": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1961": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "238": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "239": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "234": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "235": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "236": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "237": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "230": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "231": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "232": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "233": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2462": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2228": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2229": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2227": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2224": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2222": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2223": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2221": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "146": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "147": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "144": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "145": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "142": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "143": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "140": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "141": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "148": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "149": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2088": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2083": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2080": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2081": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2086": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2087": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2084": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2085": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2712": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2713": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2711": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2716": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2717": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2718": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1832": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1833": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1830": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1831": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1836": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1837": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1834": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1835": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1838": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1839": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2406": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2155": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2156": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2405": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2402": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2403": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2152": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4137": {"dna_sequence": {"fmax": "62514", "fmin": "60970", "accession": "NC_003112", "strand": "+", "sequence": "TGAACATAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGGACGGCAGCACAGAGAAGCTTGCTTCTCGGGTGGCGAGTGGCGAACGGGTGAGTAACATATCGGAACGTACCGAGTAGTGGGGGATAACTGATCGAAAGATCAGCTAATACCGCATACGTCTTGAGAGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTATTCGAGCGGCCGATATCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTCAGGGAAGAAAAGGCTGTTGCTAATATCAGCGGCTGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAATTAGCTGTTGGGCAACCTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATGTACGGAATCCTCCGGAGACGGAGGAGTGCCTTCGGGAGCCGTAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCCATCATTCAGTTGGGCACTCTAATGAGACTGCCGGTGACAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGACCAGGGCTTCACACGTCATACAATGGTCGGTACAGAGGGTAGCCAAGCCGCGAGGCGGAGCCAATCTCACAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGGGATACCAGAAGTAGGTAGGATAACCACAAGGAGTCCGCTTACCACGGTATGCTTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Neisseria meningitidis MC58", "NCBI_taxonomy_id": "122586", "NCBI_taxonomy_cvterm_id": "39597"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2401": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "933": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "932": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "931": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "937": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "936": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "935": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2409": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1955": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1954": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1957": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1956": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1951": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1950": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1953": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1952": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1959": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1958": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "829": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "828": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "825": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "824": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "827": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "826": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "821": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "820": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "823": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "822": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1483": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1482": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1481": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1480": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1487": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1486": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1485": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1484": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1489": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1488": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "797": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2411": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "795": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "794": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "793": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "792": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "791": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "929": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1719": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1718": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "799": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "798": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1270": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2412": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "613": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1272": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1139": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1138": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1133": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "616": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1131": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1130": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1137": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1136": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1135": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1134": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1276": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "476": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"4079": {"dna_sequence": {"fmax": "2150949", "fmin": "2147817", "accession": "NC_006350.1", "strand": "-", "sequence": "TCACTTGGCCTCCAGTGCCGCTTGCGCGCCGCCTCGGCGGCGCGGAACGACGTCGAACACGCGCCCGACGCAGACGAAAAAGAGCGGGACGAGGAAGATCGCGAACAGCGTCGCGCTGATCACGCCGCCGAGCACCCCCGTGCCGATCGCGATCTGCGCGCCGGATGCGGCGCCCGTCGCGAACGCGAGCGGCAGCACGCCGACGCCGAACGCGAGCGAGGTCATCACGATCGGCCGCAGCCGCAGCCGCGCGGCCTCGAGCGCCGCGTCGGCGAGCGACATGCGCTGCGCGACCAGATCCTTCGCGACCTCGACGATCAGGATCGCGTTCTTCGCGGACAAACCGATCGTCGCGATCAGCCCCACCTTGAAATAGATGTCGTTCGGCATCCCGCGCAGCGTGACGCCCGCGACCGCGCCGATCACGCCGAGCGGCACGACGAGCATCACCGCGAACGGAATCGACCAGCTCTCGTACAGCGCCGCGAGCGCGAGGAACACGACGAGCACCGACAGCGCGAACAGCATCGGCGCCTGCGCGCCCGACAGCCGCTCCTCGTACGACTGGCCGGACCACGCGTAGCCGGTGCCGGCGGGCAGCGTCGACGCGATCCGCTCGATCGCCGCCATCGCCTCGCCGCTGCTGTGCCCGGCCGACGCCGCGCCGTTGATCGTAAACGACGGAAAGCCGTTGTAGCGCGTCAACTGCGGCGGGCCCATCGTCCAGTGCAGCGTCGCGAACGCCGCGAGCGGCACCATCTCGCCCTTCGCGTTGCGCACGCGCAGCTTCGTCACGTCGGCGGCGTCGAGCCGGTGCCGCCCGTCCGCCTGCACGATCACGCGGCGCACCTGCGAGCCGTGCATGAAATCGCCGATGTAGTCCGAGCCGAACATCACAGCGAGCGTCGCGTTGATTTCCTCCATCGATACGCCGAGCGCCGACGCCTTCGCGCGATCGATGTCGAGCTTCAGCTGCGGCGCGTCCTGCGTGCCGGCGAACATCAAATCGGTCAGGACGGGGTCCTTGCGCCCCTCGGCGAGCAGCTTCTCGCGCGCGGCGACGAACGCGCCGTAGCCGAGCCCGCCGCGGTCCTGCAGCCGGAAGTCGAAGCCGCCCGTCAGGCCGAGGTCCGGCAGCGCCGGCATGTTGATCGCGAACACCATCGTGTTCGGCGTGCCGGCGAAATGCGCGTTGATCTCCGCGATGATCGCCTGCACCTGGTCCCGCGCCCGCTTGCGCTCCTTCCAGTCCTTCATCGTGACGAAGATCATCCCGCCGTTCGGCCCTTCGCCGTACAGGTTGTAGCCGCCGAGCGCGAACGTGTACGCGCTCGGCGAATGCGTGCGCACGTATTCCTCGACGCGCCGCACGCTCTGCATCGTCTCGGCGAGCGGCGTGCCCTGCGGGCGAATCACCATCACCATGAAGTTGCCCTGATCCTCGTCGGGCAGGAACGCGGCCGGCAGCTTCGTGATCAGCAGCGCGGCGGCGGCCGTCAGCGCGCCGTAGACGACGAGCCAGCGCAGCGGGCGCTCGAGCACCCGCCCGACGCGCCGCGTGTAGCGGTGCGTCGAGCGCGCGACGAAACGGTTGAACCAGCCGAAGAAGCCGTCCTTCTCGTGATGGTCGTCGGCGACGGGCTTGAGCAGCGTCGCGCAGAGCGCCGGCGTGAGCGACAGCGCGAGAAACGCCGAGAAGCCGATCGACACCGCCAGCGCGAACGCGAACTGCCGGTAGATGTTGCCGACCGCGCCGCCGAAGAACGCCATCGGCACGAACACCGACGTGAGCACGACGGTGATCCCGACGATCGCGCCGCTGATCTGCTTCATCGCCTTCACGGTGGCCTCGTACGGCGGCAGCTTCTCCTCGACCATCAGCCGCTCGACGTTCTCGACGACGACGATCGCGTCGTCGACGAGGATGCCGATCGCGAGCACCATCCCGAACATCGTCAGCACGTTGATCGAGAAGCCCGCGGCGAGCATCGCGCCGAACGTGCCGAGCAGCGCGACGGGCACGACGAGCGTCGGAATCAGCGTCGCGCGGAAGTTCTGCATGAAGAGGAACATCACCGCGAACACGAGCACGCCCGCCTCGACGAGCGTCGTGACGACCTTGCTCATCGACACGCGCACGAACGACGCCGTCTCGTACGGAATCTGGTACTTGACGCCCGGCGGAAAGAACTTCGCGAGCTCCTCCATCGTCGCGCGCACGCGCTTTTCGGTGGCGACCGCATTCGAACCGGGCGCGAGCTTGATGCCCATGCCCGTCGCCGTCTTGCCGTTCACGAACGACGGGTAGTTGTAATCGTTGCCGCCGAACTCGATTCTCGCGACGTCGCGCAGGTACAGCGTCGAGCCGTCGGCGCGCGCGCGCAGCGCGATCGCGCCGAACGCGTCGGGCGTCGTGAGCGGCGCGTCGGCGAGCACGGTCGCCGCGATCGGCGCGCTGTCGGGCACCGCGCTGCGGCCGACGTCGCCGATCGTCACGCGCGCGTTGTGCGCGCGCACGGCCGACGCGATATCGGACGCCGTCAGGCCGAGCGCCGCCATCTTCACGGGGTCCGGCCAGATCCGCATCGCATACTCGGCGCCCCAGAACTGCACCTTGCCGACGCCCTCGACGCGCCGCAGCGCCTGCAACACGTTCGCCGACGCGTATTCGCCGAGCTCCACGCCCGATAACCGTCCGTCCTCCGACGTGAGCGACACGATGATCTGCGCGTTGTCGGCCGCCTTCTCGATCGAGATGCCGTCGCGCCGCACGGGCTCGGGCAGCCGCGCCTCGACGATTTTCAGGCGGTTCTGCACGTCGACGGCCGCGAGATCGGCGCTCACGCCCTGCTTGAACGTGAGCGACAGCGACGCCTGGCCGGCGCTGCTCGTCGCCGACGTGTACAGCAGGCCGGGCACGCCGTTCATCTCGCGCTCGATCACGGCGGTGACCGATTCCTCGACGACCTGCGCGGACGCGCCCGGATACGTCGCATAGAGGCTGACGACGGGCGGCGCGATGTCCGGATACTGCGCGACGGGCAGCGCGCGGATCGCGAAGATGCCGCCCAGCATGATGAACAAGGAGATCACCCATGCGAACACCGGGCGATCGATGAAGAAACGAGCCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Burkholderia pseudomallei K96243", "NCBI_taxonomy_id": "272560", "NCBI_taxonomy_cvterm_id": "41211"}, "protein_sequence": {"accession": "YP_108402.1", "sequence": "MARFFIDRPVFAWVISLFIMLGGIFAIRALPVAQYPDIAPPVVSLYATYPGASAQVVEESVTAVIEREMNGVPGLLYTSATSSAGQASLSLTFKQGVSADLAAVDVQNRLKIVEARLPEPVRRDGISIEKAADNAQIIVSLTSEDGRLSGVELGEYASANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKMAALGLTASDIASAVRAHNARVTIGDVGRSAVPDSAPIAATVLADAPLTTPDAFGAIALRARADGSTLYLRDVARIEFGGNDYNYPSFVNGKTATGMGIKLAPGSNAVATEKRVRATMEELAKFFPPGVKYQIPYETASFVRVSMSKVVTTLVEAGVLVFAVMFLFMQNFRATLIPTLVVPVALLGTFGAMLAAGFSINVLTMFGMVLAIGILVDDAIVVVENVERLMVEEKLPPYEATVKAMKQISGAIVGITVVLTSVFVPMAFFGGAVGNIYRQFAFALAVSIGFSAFLALSLTPALCATLLKPVADDHHEKDGFFGWFNRFVARSTHRYTRRVGRVLERPLRWLVVYGALTAAAALLITKLPAAFLPDEDQGNFMVMVIRPQGTPLAETMQSVRRVEEYVRTHSPSAYTFALGGYNLYGEGPNGGMIFVTMKDWKERKRARDQVQAIIAEINAHFAGTPNTMVFAINMPALPDLGLTGGFDFRLQDRGGLGYGAFVAAREKLLAEGRKDPVLTDLMFAGTQDAPQLKLDIDRAKASALGVSMEEINATLAVMFGSDYIGDFMHGSQVRRVIVQADGRHRLDAADVTKLRVRNAKGEMVPLAAFATLHWTMGPPQLTRYNGFPSFTINGAASAGHSSGEAMAAIERIASTLPAGTGYAWSGQSYEERLSGAQAPMLFALSVLVVFLALAALYESWSIPFAVMLVVPLGVIGAVAGVTLRGMPNDIYFKVGLIATIGLSAKNAILIVEVAKDLVAQRMSLADAALEAARLRLRPIVMTSLAFGVGVLPLAFATGAASGAQIAIGTGVLGGVISATLFAIFLVPLFFVCVGRVFDVVPRRRGGAQAALEAK"}}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "1800", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1277": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "519": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "518": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "926": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1009": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1008": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1007": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1006": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "513": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1004": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "515": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1002": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1001": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "ARO_category": {"$insert": {"40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}}, "ARO_name": "Staphylococcus aureus mprF with mutation conferring resistance to daptomycin", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1000": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "623": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "622": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1225": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "620": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1223": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "626": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "625": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1220": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "629": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "628": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1229": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1228": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1535": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1561": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1286": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "11": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "10": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "13": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "12": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "15": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "14": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "17": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "16": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "19": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "18": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "928": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1534": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "201": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "200": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "203": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "202": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "205": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "204": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "207": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "206": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "209": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "208": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1573": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1572": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1571": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1570": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2231": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2230": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2233": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2232": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2235": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2234": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1576": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1575": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1574": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2185": {"$update": {"model_type": "gene cluster meta-model"}}, "2184": {"$update": {"model_type": "gene cluster meta-model"}}, "2097": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2096": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2091": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2090": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2093": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2092": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2099": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2098": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2525": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2524": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2527": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2526": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2521": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2520": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2523": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2522": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2529": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$insert": {"36696": {"category_aro_name": "antibiotic inactivation enzyme", "category_aro_cvterm_id": "36696", "category_aro_accession": "3000557", "category_aro_description": "Enzyme that catalyzes the inactivation of an antibiotic resulting in resistance.  Inactivation includes chemical modification, destruction, etc."}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2528": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2705": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2704": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2707": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2706": {"$update": {"model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1829": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1828": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1825": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1824": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1827": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1826": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1821": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1820": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1823": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1822": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2147": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2146": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2145": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2144": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2143": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2142": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4143": {"dna_sequence": {"fmax": "3825143", "fmin": "3823614", "accession": "NC_008596.1", "strand": "-", "sequence": "AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium smegmatis str. MC2 155", "NCBI_taxonomy_id": "246196", "NCBI_taxonomy_cvterm_id": "36769"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2141": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2140": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "920": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "921": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "922": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "923": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "924": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "925": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2149": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4142": {"dna_sequence": {"fmax": "3825143", "fmin": "3823614", "accession": "NC_008596.1", "strand": "-", "sequence": "AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium smegmatis str. MC2 155", "NCBI_taxonomy_id": "246196", "NCBI_taxonomy_cvterm_id": "36769"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2148": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1920": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1921": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1922": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1923": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1924": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1925": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1926": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1927": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1928": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1929": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "475": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "832": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "833": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "830": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "831": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "836": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "837": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "834": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "835": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "838": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "839": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "3": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1986": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1987": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1532": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "784": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "785": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "786": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "787": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "780": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "781": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "782": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1729": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1726": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1727": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1724": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1725": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "788": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "789": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1720": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1721": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "252": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "60": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "61": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "62": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "63": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["230", "229", "3370"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "350", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "64": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "65": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "66": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "67": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "68": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "69": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1371": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1588": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1589": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "406": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1582": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1583": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1580": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["529"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1581": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1586": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1373": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1584": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1585": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2433": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "404": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "508": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "509": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1032": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "507": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "504": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1031": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "502": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "503": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1034": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "402": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1212": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "631": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "632": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1211": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1216": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1217": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "636": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "637": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "638": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "639": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "400", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1218": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "927": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1394": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2416": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "465": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1728": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "783": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1106": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1455": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1104": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1105": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1450": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1103": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1452": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1453": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1458": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1459": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1108": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1109": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1722": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1723": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1577": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "466": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2136": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2137": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1393": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "216": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "217": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "214": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "215": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "213": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "210": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "211": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1530": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "218": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "219": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2138": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2139": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "462": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "939": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "4": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "938": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2550": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2551": {"$update": {"model_type": "gene cluster meta-model"}}, "2396": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2397": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2395": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2398": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2399": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1858": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1859": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1850": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1851": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1852": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1853": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1854": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1855": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1856": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1857": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "919": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "918": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "915": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "914": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "917": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "916": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "911": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "910": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "913": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "912": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1933": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1932": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1931": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1930": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1937": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1936": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1935": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40438": {"$update": {"param_description": "A model parameter to describe mutations in multiple genes or proteins where resistance is co-dependent on each. For example, the G247S SNP in M. tuberculosis gyrA does not confer resistance to fluoroquinolones. However, when the D500N SNP is also present in gyrB, resistance is conferred. In this case, gyrA G247S is co-dependent on gyrB D500N to confer resistance. This parameter is noted on relevant models with the following notation: [cvterm-id-gene-1],[gene-1-SNP]+[cvterm-id-gene-2],[gene-2-SNP]+ ... +[cvterm-id-gene-n],[gene-n-SNP] e.g. 39879,G247S+40052,D500N. This parameter is not currently included in any detection algorithms."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "1934": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1939": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1938": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "847": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "846": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "845": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "844": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "843": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "842": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "841": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "840": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "849": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "848": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1587": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2407": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1739": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1738": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1731": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1730": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1733": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1732": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1735": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1734": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1737": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1736": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1039": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "796": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "753": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "752": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "751": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "750": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "757": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "756": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "755": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "754": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "759": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "758": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1595": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "506": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1597": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1596": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1591": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1590": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1593": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1592": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1599": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1030": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1025": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1024": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1027": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1026": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1021": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1020": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1023": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1022": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1036": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1029": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1028": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "500": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "501": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "605": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "604": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "607": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "606": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "601": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "600": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "603": {"$update": {"ARO_description": "The MdtG protein, also named YceE, appears to be a member of the major facilitator superfamily of transporters, and it has been reported, when overexpressed, to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "602": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1205": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1204": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1207": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1206": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "609": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1200": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1203": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1202": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "633": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "634": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "635": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1214": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1215": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1447": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1110": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1445": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1444": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1115": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1442": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1117": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["242"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "500", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1116": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1119": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1118": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "467": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1449": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1448": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1219": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1357": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "460": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1355": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "489": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40394": {"$update": {"param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense SNPs truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense SNPs may be attached to models, and are recorded in the format: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "488": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "487": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "485": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "484": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "483": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "482": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "481": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "480": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "790": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "199": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "198": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "195": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "194": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "197": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "196": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "191": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "190": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "193": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "192": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1454": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1107": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1456": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2383": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1457": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2387": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2386": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1102": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1451": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1100": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1101": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "902": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "903": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "900": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "901": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "906": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "904": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "905": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1843": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1842": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "908": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "909": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1847": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1846": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1845": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1844": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2614": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1908": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1909": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1906": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1907": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1904": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1905": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1902": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1903": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$delete": ["35929"]}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1900": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1901": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "854": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "855": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "856": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "857": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "850": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "851": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}, "40394": {"$update": {"param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense SNPs truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense SNPs may be attached to models, and are recorded in the format: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "852": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "853": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "858": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "740": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "741": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "742": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "743": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "744": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "745": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "746": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "747": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "748": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "749": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1050": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1051": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1052": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1053": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1055": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1056": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1057": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1058": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1059": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1696": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1697": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1694": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1695": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1692": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1693": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1690": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1691": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1791": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1698": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1699": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1278": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1279": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "618": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "619": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "612": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1271": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "610": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "611": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1274": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "617": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "614": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "615": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1795": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1794": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1491": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1472": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1473": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1470": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1471": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1476": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1477": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1474": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1475": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1478": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1479": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1304": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1305": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1306": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1307": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1300": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1301": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1302": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}, "$insert": {"36611": {"category_aro_name": "determinant of tetracycline resistance", "category_aro_cvterm_id": "36611", "category_aro_accession": "3000472", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to tetracycline antibiotics or tetracycline-like derivatives."}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1303": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1308": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1309": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "498": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "499": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "494": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "495": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "496": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "497": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "490": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "491": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "492": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "493": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "24": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "25": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "26": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "27": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "20": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "21": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "22": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "23": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "28": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "29": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1241": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1600": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "7": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2281": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$insert": {"40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2282": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$insert": {"40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2283": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$insert": {"40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2284": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2375": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2372": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "2373": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1087": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1086": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1085": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1876": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1877": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1874": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1875": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1872": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1873": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1870": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1871": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1083": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1878": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1879": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "977": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "976": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "975": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "974": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "973": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "972": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "970": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1080": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "979": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "978": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "182": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "183": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "180": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "181": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "186": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "187": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "184": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "185": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2110": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2111": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "188": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "189": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2114": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2115": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2116": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "1559": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1919": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1918": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1911": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1910": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1913": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1912": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1915": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1914": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1917": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1916": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "869": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "868": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2113": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "861": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "860": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "863": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "862": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "865": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "864": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "867": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "866": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2024": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2025": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2026": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2027": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2020": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2021": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2022": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2023": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2117": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2028": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2029": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1502": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "883": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "882": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "881": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["499", "506", "504", "505", "502", "503", "500"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "880": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "887": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "886": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "885": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "884": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "889": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "888": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1503": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "775": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "774": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "777": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "776": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "771": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "770": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "773": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "772": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "779": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "778": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "77": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "76": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "75": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "74": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "73": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "72": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "71": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "70": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "79": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "78": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1043": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1042": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1041": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1040": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1047": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1046": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1045": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["550"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "450", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1044": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1049": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1048": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1681": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1680": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1683": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1682": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1685": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1684": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1687": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1686": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1689": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1688": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1269": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1268": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "669": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "668": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "667": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1262": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "665": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "664": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "663": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "662": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1265": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1264": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "640": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1469": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1468": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "520": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1467": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1466": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1461": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1460": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1463": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1019": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1317": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1316": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1315": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1314": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1313": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1312": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1311": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1310": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1319": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1318": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1010": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "464": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1011": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "319": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "318": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "313": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "312": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "311": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "310": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "317": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "316": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "315": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "314": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2756": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2754": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1335": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2755": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1334": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2752": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1337": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2753": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1336": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2750": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1331": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2751": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1330": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1333": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1332": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2324": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "630": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2298": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2292": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2291": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2290": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2294": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "403": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1521": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "659": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1612": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1861": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1860": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1863": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1862": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1865": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1864": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1867": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1866": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1869": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1868": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "964": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "965": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "966": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "967": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "960": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "961": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "962": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "963": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "401": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "968": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "969": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2109": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40438": {"$update": {"param_description": "A model parameter to describe mutations in multiple genes or proteins where resistance is co-dependent on each. For example, the G247S SNP in M. tuberculosis gyrA does not confer resistance to fluoroquinolones. However, when the D500N SNP is also present in gyrB, resistance is conferred. In this case, gyrA G247S is co-dependent on gyrB D500N to confer resistance. This parameter is noted on relevant models with the following notation: [cvterm-id-gene-1],[gene-1-SNP]+[cvterm-id-gene-2],[gene-2-SNP]+ ... +[cvterm-id-gene-n],[gene-n-SNP] e.g. 39879,G247S+40052,D500N. This parameter is not currently included in any detection algorithms."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "2108": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2103": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2102": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4126": {"dna_sequence": {"fmax": "5029475", "fmin": "5027947", "accession": "NC_008596.1", "strand": "-", "sequence": "AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium smegmatis str. MC2 155", "NCBI_taxonomy_id": "246196", "NCBI_taxonomy_cvterm_id": "36769"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_value": {"7816": "U2362C", "7814": "U1389C", "7815": "C2360U"}, "clinical": {"7816": "U2362C", "7814": "U1389C", "7815": "C2360U"}, "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2100": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2106": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4144": {"dna_sequence": {"fmax": "3825143", "fmin": "3823614", "accession": "NC_008596.1", "strand": "-", "sequence": "AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium smegmatis str. MC2 155", "NCBI_taxonomy_id": "246196", "NCBI_taxonomy_cvterm_id": "36769"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2105": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2104": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1560": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "641": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "878": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "879": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "876": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "877": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "874": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "875": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "872": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "643": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "870": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "871": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2037": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2036": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2035": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1242": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2745": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"blastp_bit_score": {"param_value": "2661,1104,826,2306,431,1922,2776,228,2066,520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}}, "2744": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2031": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2030": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "9": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2748": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "2039": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "644": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "890": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "891": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "892": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "893": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "894": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "895": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "896": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "897": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "898": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "899": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "646": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1249": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "648": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1964": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1965": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1966": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1788": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1789": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "768": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "769": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1780": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1781": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "760": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "761": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "766": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "767": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "764": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "765": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1962": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1963": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1078": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1079": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1076": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1077": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1074": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1075": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1072": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1073": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1070": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1071": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1678": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1679": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1674": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1675": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1676": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1677": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1670": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1671": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1672": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1673": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1094": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1095": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1096": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1097": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1090": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1091": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1092": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1093": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["266"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "325", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "674": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "675": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "676": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "677": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1098": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1099": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "672": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "673": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1997": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1533": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1418": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1419": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1410": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1411": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1412": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1413": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1414": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1415": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1416": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1417": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1322": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1323": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1320": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1321": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1326": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1327": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1324": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1325": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1328": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1329": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "5": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1531": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1256": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1257": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1254": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1255": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1520": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1253": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1250": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1251": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1528": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1529": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1258": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1259": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "308": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "309": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "300": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "301": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "302": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "303": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "304": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "305": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "306": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "307": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1792": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "473": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "_timestamp": "2017-08-03T15:06:40+00:00", "2478": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4114": {"dna_sequence": {"fmax": "1512657", "fmin": "1511156", "accession": "CP003904.1", "strand": "-", "sequence": "AGGAGGTGATCCAACCGCAGGTTCACTACGGTTACCTTGTTACGACTTCACCCCAGTCGCTGTGTGTGCCGTGGGCAGTAGCCAATTTAGCATCCTGACTTAAGGCAAACACAACTCCCATGGTGTGACGGGCGGTGAGTACAAGACCCGGGAACGTATTCACCGCAACATGGCTGATTTGCGATTACTAGCGATTCCAGCTTCATGCAGGCGAGTTGCAGCCTACAATCCGAACTGAGAGGTGTTTTGAAGATTGGCTCCATTCGCAGTATTGCTTCTCTTTGTGCACCCCATTGTAGCACGTGTGTAGCCCTAGGCGTAAGGGCCATGATGACTTGACGTCGTCCCCACCTTCCTNCCCTTACGGAGGCAGTATCCTTAGAGTTCTCAGCATAACCTGTTAGCAACTAAGAAAAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCGTGCAGCACCTGTTTTCAAGGTCTGGCAAGCCAGACACTCCACTATTTCTAGCGGATTCTCTCAATGTCAAGCCTAGGTAAGGTTCTTCGTGTATCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGTCCCCGTCTATTCCTTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGGATGCTTAATGCGTTAGCTGCATTACTGGAGAGACTAAGCCCTCCAACAACTAGCATCCATCGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCAACMGCTTTCGCGCAATCAGCGTCAGTAATGTTCCAGCAGGTCGCCTTCGCAATGAGTATTCCTCTTGATCTCTACGGATTTTACCCCTACACCAAGAATTCCACCTACCTCTCCCACACTCTAGAATAGTAGTTTCAAATGCAGTTCTATGGTTAAGCCATAGGATTTCACACCTGACTGACTATCCCGCCTACGCGCTCTTTACGCCCAGTGATTCCGAGTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTATTCGTTAGATACCGTCATTATCTTCTCTAACAAAAGGAGTTTACAATCCTAAAACCTTCATCCTCCACGCGGCGTTGCTGCTTCAGGGTTTCCCCCATTGAGCAATATTCCCTACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGTCCGTTCACCCTCTCAGGCCGGATACCCGTCATAGCCTTGGTAAGCCATTACCTTACCAACAAGCTGATAGGACATAGGCTGATCTCTTAGCGATAAATCTTTCCCCCGTAGGAGTATCTGGTATTAATCATCGTTTCCAATGGCTATCCCAAACTAAGAGGCACATAACCTATGCGTTACTCACCCGTGCGCCACTAATCAGCACTCTAGCAAGCTAGAAGCTTCATCGTTCGACTTGCATGTATTAGGCACGCCGCCAGCGTTCACTCTGAGCCAGGATCAAACTCTCCATAAAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Helicobacter pylori 26695", "NCBI_taxonomy_id": "85962", "NCBI_taxonomy_cvterm_id": "36758"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "470": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "471": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1898": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1899": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1894": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1895": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1896": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1897": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1890": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1891": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1892": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1893": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "959": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "958": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2134": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2135": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2132": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2133": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2130": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2131": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4123": {"dna_sequence": {"fmax": "1473382", "fmin": "1471845", "accession": "AL123456.3", "strand": "+", "sequence": "TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332", "NCBI_taxonomy_cvterm_id": "39507"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_value": {"$delete": ["4803"], "$insert": {"7820": "C516U"}}, "clinical": {"$delete": ["4803"], "$insert": {"7820": "C516U"}}, "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "951": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "950": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "952": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "955": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "954": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "957": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "956": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "477": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2643": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2644": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2645": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2646": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2002": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2003": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2000": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2001": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2006": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2007": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2004": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2005": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2008": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2009": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2034": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1263": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "666": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2176": {"$update": {"model_type": "gene cluster meta-model"}}, "1261": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2177": {"$update": {"model_type": "gene cluster meta-model"}}, "1799": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1798": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "719": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "718": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "717": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1267": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "715": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "714": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "713": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "712": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "711": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "710": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "661": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "716": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "505": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"40394": {"$update": {"param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon. Nonsense SNPs truncate protein translation prematurely, resulting in a defective or completely inactive protein. In CARD, nonsense SNPs may be attached to models, and are recorded in the format: [wild type amino acid][position][STOP] (e.g. Q42STOP). This parameter is not currently used in detection algorithms."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "660": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2178": {"$update": {"model_type": "gene cluster meta-model"}}, "1069": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1068": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2179": {"$update": {"model_type": "gene cluster meta-model"}}, "1061": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1060": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1063": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1062": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1065": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1064": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1067": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1066": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1669": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1668": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1667": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1666": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1665": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1664": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1663": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1662": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1661": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1660": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "591": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "590": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "593": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "592": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "595": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "594": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "597": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "596": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "599": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "598": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1089": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1088": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1526": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1409": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1408": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1403": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1402": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1401": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1400": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1407": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1406": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1405": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1404": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1546": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "449": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "448": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1339": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1338": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1547": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "443": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "442": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "441": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "440": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "447": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "446": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "445": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "444": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1545": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "1542": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"4080": {"dna_sequence": {"fmax": "2152165", "fmin": "2150965", "accession": "NC_006350.1", "strand": "-", "sequence": "TCAGGTTGAGCGCCGGCCGGGCGCGGAAGCCGCGGCGGCGCCGGAGGCCGGCTGCGCGGCGGCGCCGCGCTCGAGCGCCTTCACCGTCGTGCCTGCTTCGAATTGCGCGGCGTCGACGACGACGACGCGCTCGCCGCCCGCGAGCCCGCGCGTGACGATCCAGTCGCGGCCTTTCATCTGCGCGGCCTCGACCGTCACGTCGCGTATCTTGCCGTTCTGGCCGACGACCTTGACGGTCGCGCTGTCGGCCGTGCGCAGCAGCGCGTCGCGCGGCACGAGGATCGCGTCGCGCGCGACCGCGCGATCGAGCGCGATCCGCACGTACGCGCCGGGCAGCAGTTCGCGCTCCGGGTTCGGAAAGAGCGCACGCATCGCCACCGTGTCGGTGGACGGGTCGACGGCAAGATCCGCGAACAGCAGCTTGCCCTTGCGCGCGTACGTGCTGCCGTCCGGGCGCACGAGCGTCACCTCGACGTCCTGCTGCGCGATGCCCGCCGCGCGTCCGCTCTTCACCGCGCGCCGCAGCGATTCGACGTCGGCCGCGGGCTGCGAGAAGTTCACGTAGATCGGATCGAGCTGCTCGACGGTCGTGAGCGGCGTCGCCTGATCCTGGCCGACGAGCGCGCCTTCGGTCACGAGCGCGCGGCGCGCGCGGCCGTCGATCGGCGCGGTGACGGTCGCGTAATCGAGCTGCAGTTGCGCGCGCGCGAGCTCCGCGCGCGCCGACGCGACGGCCGCCTTCGCCTGCCGTTCGTCGGCGAGCGCCTCGGTGTGGTCGCGCTCGCTGACCGCGCGGTCGCGCACGAGCTCGTCATAGCGGCGGCGCTTGTCGAGCGCCGCGAGGTGCGCGGCCCGCGCCTTCTCGAGCGCGCCCGCGGCCGCGTCGCGCGCCGCCTTGAACGGCGCGGGATCGATCCTGAACAGCACCGCGCCGCGCTTGACTTCCTGCCCTTCCTCGTAGGTGCGCGCGGTCACGATGCCCGCGACCCGCGCGCGCACCTCGGCCTGCCGGTACGCGTCGAGCCGGCCCGGCAATTCGACCGACAGCGGCACCGATGTCTTCTTCACCGTGACGACGCTCGCCTCGCGCGGCGCGGCGGCGTCGTGCTCGCTTTCGTGCTTGCCGCAGCCGGCCGCGACGAACGCCGCGACCGCGAGCGCCGCCGACAAGCGGCGCGTGCGTGCCCATTCGTATTTCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Burkholderia pseudomallei K96243", "NCBI_taxonomy_id": "272560", "NCBI_taxonomy_cvterm_id": "41211"}, "protein_sequence": {"accession": "YP_108403.1", "sequence": "MKYEWARTRRLSAALAVAAFVAAGCGKHESEHDAAAPREASVVTVKKTSVPLSVELPGRLDAYRQAEVRARVAGIVTARTYEEGQEVKRGAVLFRIDPAPFKAARDAAAGALEKARAAHLAALDKRRRYDELVRDRAVSERDHTEALADERQAKAAVASARAELARAQLQLDYATVTAPIDGRARRALVTEGALVGQDQATPLTTVEQLDPIYVNFSQPAADVESLRRAVKSGRAAGIAQQDVEVTLVRPDGSTYARKGKLLFADLAVDPSTDTVAMRALFPNPERELLPGAYVRIALDRAVARDAILVPRDALLRTADSATVKVVGQNGKIRDVTVEAAQMKGRDWIVTRGLAGGERVVVVDAAQFEAGTTVKALERGAAAQPASGAAAASAPGRRST"}}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "500", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1543": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "39": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "38": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1540": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "33": {"$update": {"ARO_description": "MsrE is an ABC-efflux pump expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species.", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "32": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "31": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "30": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "37": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "36": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "35": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "34": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1537": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1536": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1243": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "642": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "645": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1244": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "647": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1246": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "649": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1248": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1539": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1538": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "339": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "338": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "335": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "334": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "337": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "336": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "331": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "330": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "333": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "332": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2032": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "8": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1464": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2119": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1462": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1889": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1888": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1887": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1886": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1885": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1884": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1883": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1882": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1881": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1880": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2121": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2123": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2122": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2124": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "948": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "949": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "946": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "947": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "944": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1084": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "942": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "943": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "940": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "941": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2410": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2659": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2653": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2656": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2655": {"$update": {"ARO_description": "EmrE is a small multidrug transporter that functions as a homodimer and that couples the efflux of small polyaromatic cations from the cell with the import of protons down an electrochemical gradient. Confers resistance to tetraphenylphosphonium and methyl viologen.", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2654": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "133": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "132": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "131": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "130": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "137": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "136": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "135": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "134": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "139": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1354": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2019": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2018": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2015": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2014": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2017": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2016": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2011": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2010": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2013": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2012": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1793": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2112": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "934": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "708": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "709": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "704": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "705": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "706": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "707": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "700": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "701": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "702": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "703": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "88": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "89": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "82": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "83": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "80": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "81": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "86": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "87": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "84": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "85": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "762": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1658": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1659": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1652": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1388": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1650": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1651": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1656": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1657": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1654": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1655": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "586": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "587": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "584": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "585": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "763": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "583": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "580": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "581": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1984": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "588": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "589": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1985": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1982": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1983": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1436": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1437": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1434": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1432": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "40330": {"$update": {"param_description": "A set of nucleotide or amino acid substitutions that are each required to confer resistance to an antibiotic drug or drug class by co-mutation. Compare to single resistance variant, where only one substitution is required. Multiple resistance variants parameters are indicated on appropriate models using the following notation: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2],...,[wild-type n][position n][mutation n]. When each included substitution is detected in a protein sequence, resistance is conferred. This parameter is not currently included in any detection algorithms."}}}, "$delete": ["blastp_evalue"]}}}, "1433": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1430": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1431": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "418": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1981": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1438": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1381": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1260": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1349": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1541": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "458": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "459": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "450": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "451": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "452": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1343": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1344": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "455": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "456": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "457": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1082": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "517": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1266": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "656": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "657": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "654": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "655": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "652": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "653": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "650": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1505": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1508": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1509": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "658": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "516": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1992": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2127": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2126": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2129": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2128": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "945": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1376": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1081": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "322": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "323": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "320": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "321": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "326": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "327": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "324": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "325": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "329": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1340": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2330": {"$update": {"ARO_description": "leuO, a LysR family transcription factor, exists in a wide variety of bacteria of the family Enterobacteriaceae and is involved in the regulation of as yet unidentified genes affecting the stress response and pathogenesis expression. LeuO is also an activator of the MdtNOP efflux pump.", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$insert": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2331": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2332": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "2250", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2333": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2335": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1594": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1341": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1995": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2482": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4108": {"dna_sequence": {"fmax": "40023", "fmin": "38549", "accession": "NC_005353.1", "strand": "+", "sequence": "ATCCATGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGAGCAAAGCAATTTGTGTAGTGGCGAACGGGTGCGTAACGCGTAAGAACCTACCTATCGGAGGGGGATAACATTGGGAAACTGTTGCTAATACCCCATACAGCTGAGGAGTGAAAGGTGAAAAACCGCCGATAGAGGGGCTTGCGTCTGATTAGCTAGTTGGTGGGGGTAACGGCCTCCCAAGGCCACGAGCAGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTTCGCAATGGGCGCAAGCGACGGAGCAATGCCGCGTGCAGGAAGAAGGCCTGTGGGTCGTAAACTGCTTTTCTCAGAGAAGAAGTTCTGACGGTATCTGAGGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTGTCCGCAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTCGTAAAGTCTAATGTCAAATACCAGGGCTCAACCTTGGACCGGCATTGGAGTACTCACGAGCTTGAGTACGGTAGGGGCAGAGGGAATTCCATGTGGAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGCTCTGCTGGGCCGAAACTGACACTGAGAGACGAAAGCTGGGGGAGCGAATAGGATTAGATACCCTAGTAGTCCCAGCCGTAAACTATGGAGACTAAGTGCTGCCGCAAGCAGTGCTGTAGCTAACGCGTTAAGTCTCCCGCCTGGGGAGTATGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGACCGCACAAGCGGTGGATTATGTGGATTAATTCGATACAACGCGAAGAACCTTACCAGGGTTTGACATGTCAAGAACCTCTCAGAAATGGGAGGGTGCCCTAACGGACTTGAACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGCTGTGAAGTGTATAGTTAAGTCTCATAACGAGCGCAACCCTCGTCTTTAGTTGCCATTTGGTTCTCTAAAGAGACTGCCAGTGTAAGCTGGAGGAAGGTGAGGATGACGTCAAGTCAGCATGCCCCTTACATCCTGGGCTTCACACGTAATACAATGGTTGGGACAATCAGAAGCGACTCGTGAGAGCTAGCGGCTCTGTTAAACCCAACCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCCGGAATCGCTAGTAATCGCCAGTCAGCTATATGGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGAAGCTGGTTCTGCTCCAAGTCGTTACCCTAACCTTCGGGAGGGGGGCGCCTAAAGCAGGGCTAGTGACTAGGGTGAAGTCGTAACAAGGTAGGGCTACTGGAAGGTGGCCCTGGCTCACCTCCTTC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Chlamydomonas reinhardtii", "NCBI_taxonomy_id": "3055", "NCBI_taxonomy_cvterm_id": "40815"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "1598": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2248": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2249": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2244": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2245": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2246": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2240": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2241": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2242": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2243": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "995": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "994": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "997": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "996": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "991": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "990": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "993": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "992": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "999": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "998": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "120": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "121": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$delete": ["35929"]}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "122": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "123": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "124": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "125": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "126": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "127": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "128": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "129": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2068": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2069": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2060": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2061": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2062": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2063": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2064": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2065": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2066": {"$update": {"model_type": "protein overexpression model", "model_description": "This model detects protein overexpression based on the presence of mutations.The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}, "model_type_id": "41091"}}, "2666": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2660": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2661": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1748": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1749": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1645": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1644": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1647": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1646": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1641": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1640": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1643": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1642": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1396": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1649": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1648": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1742": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1743": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1252": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "579": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "578": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "573": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "572": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "571": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "570": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "577": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "576": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "575": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "574": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1209": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1208": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1421": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1420": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1423": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1422": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1425": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1424": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1427": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1426": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1429": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1428": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2404": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "731": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "730": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2157": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "735": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "734": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "737": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "736": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "739": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "738": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1359": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1358": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "469": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "468": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1353": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1352": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1351": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1350": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "461": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1356": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "463": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "608": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1273": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2158": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1519": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1518": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1515": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1514": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1517": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1516": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1511": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1510": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1513": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1512": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1275": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "280": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "582": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "357": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "356": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "355": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "354": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "353": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "352": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "351": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "350": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "359": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "358": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1033": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2323": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1111": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2321": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2326": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2325": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1446": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2329": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2328": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1113": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["3593"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "289": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "288": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1112": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "281": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1443": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "283": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "282": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "285": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "284": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "287": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1114": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1441": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1440": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "263": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "262": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "261": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "260": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "267": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "266": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "265": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "264": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "286": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "269": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "268": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1562": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1563": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1564": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2192": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1565": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1566": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2259": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2257": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1567": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["3612"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "225", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2251": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2476": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_value": {"7809": "A633G", "7810": "C734U", "7811": "C735U"}, "clinical": {"7809": "A633G", "7810": "C734U", "7811": "C735U"}, "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2600", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "988": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "989": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_sequences": {"$update": {"sequence": {"$delete": ["589"]}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "982": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "983": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "980": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "981": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "986": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "987": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "984": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "985": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "115": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "114": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1790": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "116": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "111": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "110": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "113": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "112": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "119": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "118": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1797": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2079": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2078": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2500", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2073": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2072": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2071": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2070": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2077": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4145": {"dna_sequence": {"fmax": "3825143", "fmin": "3823614", "accession": "NC_008596.1", "strand": "-", "sequence": "AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Mycobacterium smegmatis str. MC2 155", "NCBI_taxonomy_id": "246196", "NCBI_taxonomy_cvterm_id": "36769"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2076": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_sequences": {"$update": {"sequence": {"4136": {"dna_sequence": {"fmax": "385288", "fmin": "383737", "accession": "CP020418", "strand": "+", "sequence": "AGAGATTGAACATAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGGACGGCAGCACAGGGAAGCTTGCTTCTCGGGTGGCGAGTGGCGAACGGGTGAGTAACATATCGGAACGTACCGGGTAGCGGGGGATAACTGATCGAAAGATCAGCTAATACCGCATACGTCTTGAGAGGGAAAGCAGGGGACCTTCGGGCCTTGCGCTATCCGAGCGGCCGATATCTGATTAGCTGGTTGGCGGGGTAAAGGCCCACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTCAGGGAAGAAAAGGCCGTTGCCAATATCGGCGGCCGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGATAACACTGACGTTCATGTCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAATTAGCTGTTGGGCAACTTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGTTTTGACATGTGCGGAATCCTCCGGAGACGGAGGAGTGCCTTCGGGAGCCGTAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCCATCATTCGGTTGGGCACTCTAATGAGACTGCCGGTGACAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGACCAGGGCTTCACACGTCATACAATGGTCGGTACAGAGGGTAGCCAAGCCGCGAGGCGGAGCCAATCTCACAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGGGATACCAGAAGTAGGTAGGGTAACCGCAAGGAGTCCGCTTACCACGGTATGCTTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCTA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Neisseria gonorrhoeae", "NCBI_taxonomy_id": "485", "NCBI_taxonomy_cvterm_id": "36806"}, "protein_sequence": {"accession": "", "sequence": ""}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_value": {"7828": "C1198U"}, "clinical": {"7828": "C1198U"}, "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "2075": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2074": {"$update": {"model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "model_param": {"$update": {"snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["41093"], "$insert": {"blastn_bit_score": {"param_value": "2700", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}}}}}, "1796": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1035": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1389": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2679": {"$update": {"model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "model_param": {"$update": {"41141": {"$update": {"param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}}}}}, "1630": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1631": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1632": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1633": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1634": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1635": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1636": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1637": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1638": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1639": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1988": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1989": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "568": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "569": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "560": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "561": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "562": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "563": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "564": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "565": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "566": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "567": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1188": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1189": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1186": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1187": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1184": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1185": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1182": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1183": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1180": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1181": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "726": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "727": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "724": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "725": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "722": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "723": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "720": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "721": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1745": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1746": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1747": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1740": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1741": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "728": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "729": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1164": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1165": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1166": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1167": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1160": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1161": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1162": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1163": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1168": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1169": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "48": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "49": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "46": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "47": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "44": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "45": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "42": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "43": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "40": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "41": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1568": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1569": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1298": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1299": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1292": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1293": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1290": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1291": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1296": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1297": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1294": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1295": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1713": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_category": {"$update": {"36021": {"$update": {"category_aro_name": "protein(s) conferring antibiotic resistance via molecular bypass", "category_aro_description": "Proteins involved in restructuring of the cell wall, causing antibiotic resistance."}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1360": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1712": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2033": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1711": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "2425": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1710": {"$update": {"model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "snp": {"$update": {"param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1717": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1716": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1715": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "732": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1201": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1714": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "472": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1367": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1364": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1365": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1362": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1363": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "474": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1361": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "478": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "479": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1368": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}, "1369": {"$update": {"model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}}, "$delete": ["blastp_evalue"]}}}}, "$delete": ["2275", "1465", "930", "2273", "2322"], "$insert": {"2778": {"model_id": "2778", "ARO_accession": "3004110", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "MCR-2 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting in reduction of the negative charge of the cell membrane. Originally identified in a Belgian sample of Escherichia coli by Xavier et al, (2016).", "model_sequences": {"sequence": {"4094": {"dna_sequence": {"fmax": "1717", "fmin": "100", "accession": "NG_051171.1", "strand": "+", "sequence": "ATGACATCACATCACTCTTGGTATCGCTATTCTATCAATCCTTTTGTGCTGATGGGTTTGGTGGCGTTATTTTTGGCAGCGACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTGGCGGTGATGGGTGCTATGCTACTGATTGTCGTGCTGTTATCCTATCGCTATGTGCTAAAGCCTGTCCTGATTTTGCTACTGATTATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGACACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAGGACTTGATGAATTTGGCGTTTTTTGTGCGAATTATCGGGCTTGGCGTGTTGCCAAGTGTGTTGGTCGCAGTTGCCAAAGTCAATTATCCAACATGGGGCAAAGGTCTGATTCAGCGTGCGATGACATGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGACTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAACCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCGCCAACAGACACCATCTATCATGCCAAAGACGCCGTGCAGACCACCAAGCCGAGCGAGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCGCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGTGAGACTTTCCCGCAGCTTGCCAAAGTTGATGGCTTGGCGAATTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATTTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGTGTGGGTATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTACCTGCCACGCAGTATTTTGATTATAAATCAGCAACCAACAATACCATCTGTAACACCAATCCCTATAACGAATGCCGTGATGTCGGTATGCTTGTCGGGCTAGATGACTATGTCAGCGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCCGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACACCAATCACTCATCAATGCCTATGACAATGCGCTACTTGCGACTGATGATTTTATCGCCAAAAGCATCGATTGGCTAAAAACGCATGAAGCGAACTACGATGTCGCCATGCTCTATGTCAGTGACCACGGCGAGAGCTTGGGCGAAAATGGTGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCTGTGCCTGCGTTTTTTTGGTCAAATAATACGACATTCAAGCCAACTGCCAGCGATACTGTGCTGACGCATGATGCGATTACGCCAACACTGCTTAAGCTGTTTGATGTCACAGCGGGCAAGGTCAAAGACCGCGCGGCATTTATCCAGTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "WP_065419574.1", "sequence": "MTSHHSWYRYSINPFVLMGLVALFLAATANLTFFEKAMAVYPVSDNLGFIISMAVAVMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSVLVAVAKVNYPTWGKGLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTTFKPTASDTVLTHDAITPTLLKLFDVTAGKVKDRAAFIQ"}}}}, "ARO_category": {"39418": {"category_aro_name": "determinant of polymyxin resistance", "category_aro_cvterm_id": "39418", "category_aro_accession": "3002984", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to polymyxin antibiotics, i.e. colistin."}, "40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}, "ARO_name": "MCR-2", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41231", "model_name": "MCR-2", "model_type_id": "40292"}, "2779": {"model_id": "2779", "ARO_accession": "3004111", "model_param": {"blastp_bit_score": {"param_value": "280", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "fosA6 is a plasmid-encoded enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.", "model_sequences": {"sequence": {"4095": {"dna_sequence": {"fmax": "620", "fmin": "0", "accession": "NG_051497.1", "strand": "+", "sequence": "CCGGCTTTGAGATGCTGATGCTGTGGCACGAGCGCTGGCACCGCGACCCGGCGCATCAATGGCTGCGTCAGTTCATTGTGAATTCACTGGAGGAACAGACATGCTGAGTGGACTGAATCACCTGACCCTGGCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGCTGGGCATGACGCTGCATGCCCGCTGGGACAGCGGGGCTTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCGCTGGATCCGCAGCGGCGCGTTACTCCGCCGGAAGAGAGCGACTACACCCATTATGCGTTTAGTATTAGCGAAGCCGATTTTGCTAGCTTCGCCGCCCGCCTTGAGGCTGCCGGCGTGGCGATCTGGAAGCTGAACCGTAGCGAAGGTGCCTCGCACTATTTCCTCGATCCCGATGGCCATAAGCTGGAGCTGCACGTCGGCAGTCTCGCCCAGCGTCTGGCCGCCTGCCGCGAACAGCAGTATAAGGGGATGGTGTTTTTTGATCAGTGAAGCTGCTTCGCAGACGCTAGATCACCCGTAGCCCCGGTAAGCGCAGCTCCACCGGGGAGAACAGGTTAAATTCACTCCATCGCCACCTTCACCGCTTCTC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "WP_069174570.1", "sequence": "MLSGLNHLTLAVSQLAPSVAFYQQLLGMTLHARWDSGAYLSCGDLWLCLSLDPQRRVTPPEESDYTHYAFSISEADFASFAARLEAAGVAIWKLNRSEGASHYFLDPDGHKLELHVGSLAQRLAACREQQYKGMVFFDQ"}}}}, "ARO_category": {"36696": {"category_aro_name": "antibiotic inactivation enzyme", "category_aro_cvterm_id": "36696", "category_aro_accession": "3000557", "category_aro_description": "Enzyme that catalyzes the inactivation of an antibiotic resulting in resistance.  Inactivation includes chemical modification, destruction, etc."}, "36410": {"category_aro_name": "determinant of fosfomycin resistance", "category_aro_cvterm_id": "36410", "category_aro_accession": "3000271", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to fosfomycin antibiotics."}}, "ARO_name": "FosA6", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41232", "model_name": "FosA6", "model_type_id": "40292"}, "2759": {"model_id": "2759", "ARO_accession": "3004100", "model_param": {"blastp_bit_score": {"param_value": "1700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LpeB is a subunit of the LpeAB efflux pump in Legionella pneumophila, which is homologous to AcrB in E. coli.", "model_sequences": {"sequence": {"4076": {"dna_sequence": {"fmax": "3284910", "fmin": "3281865", "accession": "CR628336.1", "strand": "+", "sequence": "ATGAAACTCACCAGCTATTTCATCAAACATCCTGTAATCACCATCATCTTAAACGCCATGATTGTTGTTCTGGGGTTATTATGTCTCTATAATTTATCCGTTAGGGAATATCCTGATATCAATTTTCCTACAATAACTGTTTCAGCAAGCTACCCCAACGCCAGTCCCGATTTAGTTGAAACCGCAATAACCAATGTTCTGGAGGACCGTCTTGCAGGTATAGAAGGGTTAGAAACAATTACGTCGCAATCAAGTGCAGGCTATGCGCAAATCACCTTGATGTTTCGTTCCGGAACATCCATGGATAGAGCACTGAGTACCACTCAAGACGCCGTAGGAGTAGCCAAAGCACTTCTGCCACCGGAGGTAAGATCGCCAACAGTTGAACGCCAACGCAAATCCAATGGCCTTCCTTTTATTGGGATTTCATTGGAATCAACATCCAAAGACTTTGGTGAGCTGACTCATTACGCTAATCTTAATTTAAAAAATGTCTTTCGCAGTGTGCAAGGTGTTGCTTCCGTTGAAGTATGGGGGCAACCCTATACATACAACATTACCCTTCAACCTGAAAAATTATTTTCTTTTGGAGTTAATGTTGATGAAATAGTGAATGCGCTCGCAAAAAATCGTATTTCGTTGCCCGCAGGTAATTATAGAAATAAAATTCCCAGTACTCTTAATTCTGAGCTGAAAACCCGGGAAGATTATGAGAATCTTTTAATCAAGGCAAATTCCAAACATCCCATTTTACTCAAATCACTGGCTAATGTCGCATTGGAAACCGATAACTCACAAATGCGAGTTCGCGTTAATGGGCACGCTGGTGTTGTGCTTTCTATCAATAAAGCGAATGAAGCCAATCCTATTGAAGTCTCTAAAGAAATTAGAAAAGTGATTAAAGGATTACAACAAGGGTTGCCCAAGGATCTGAAAATAAACACTATTATTGATCAATCGGATTTTATTAATGCCTCCATTAAAAACATTAGATCCGCGATTGGTGAAGCCATTTTTTTAGTCTTAATCATAGTCTTCCTTTTTTTACGTAATATTAAAGCCACCATCATCCCTCTAATTACCATTCCAATTTCATTATTGGGGTCCTTGCTTTTCCTTAAATTGTTTGGTTTTTCAATCAATTTAATGACCTTACTGGCTATGGTATTGGCAATCGGTTTGGTTGTAGACGATGCGATTATTGTCTTGGAAAACATTTGGCGTCATATTGAAAGCGGATTATCTCCTTTGGATGCTGCGCTTAAAGGAGCACGTGAAATTGGCTTCGCCATTATAGCGATGACATTTACCCTTAGCAGTGTTTATTTGCCTATAGCCTTTATCCAGGGGATGCTGGGACAGCTCTTCGTTGAATTTGCTGTTGCTCTGGCAGGCAGTGTTTTCATTTCGGGGATTGTTGCCCTGACACTTTCACCATTGATGTGTGCCAACCTTTTGAGTGCATCTTCTAAAAACTGGTGGCCACAATTCGATAATGCTCTTGAAAAGTTAACTAAACATTACTCCAATATTTTACAATTCATTCTGAAACACCAAAAGATTACTTTGCTAACAGCTCTAATTTCTGTCGTTGCTTGCTTTGGATTTTATAATTTAATTAGCCATGAAACCGCTCCTAAAGAAGATCGAGGTTTAATAGGTATTTATATCCCTCCTGTAGCAGGAGAAGACATAGGGATGTTGGACAACAAAACAGGAAAACTTGAAAAAAAACTAGATGCCATCCCCGAGGCAAATAATCGCCTGACTTTTATTGGTGACTGGGGCGGGTCAATAGTACTGCCATTAAAACCTCATGCTCAACGTCATCGAAGTGCGAACCAGATTGTTGAGAAATTAAGACCTTCTTTTAACCACTTCCCCTCCATGGATCCTCATGTATGGAGTTGGGATACAGGCTTACCAGGAGTTGATGATGCCGGGAGTGGATCTGAATTGACTCTGGTTATTTCTACCCCAGACCATTTCAGGCAATTATTTGATGAAACTGAAAAATTAAAAAGTGTTCTAGACAAGAGCAAATTATTTGCAGCAGTGAACTATGACCTTCGCCTTGATACCATGGGATACAATATAGACCTTGATTATAACCAACTGGCGAAACTTGGACTGACAGCAAATCAGGTGGCAAAGACGATTGAGGTATTTTTCAGTGGCGACAAGTCACAAACCTTTGAAAAAGATGGGGTCGTTTATAATATATCGATTAAAGGAGATTCCTCCCCCTGGACTTTGAATGAACTTTATTTAACTACAAATGAAGGGAAGTCTGTTTCATTGGGAGCTATTACCAAAATGCAGCCCAAGGCTCAACCGGCAACTCTTGATCATTATCAGCAAATGCGTTCGACCACTCTCCATGTCCAATTACATAAGGGAGACTCTATGGCAAAGGCTATTGAAAAATTATGGGGCACTACCAAAGAAGTGATGCCTCAACACTATAAACTGACCTGGATTGGTGCGGCCAAAGCATTCCATGAATCTTCCAATTCCATGTTATTTTTGTTTTTCTTATCTTTGGCTTTCATCTATGCCATTTTATGCACACAATTCGAGAATTTTACTGACCCCTTCATTATTCTATTCACTGTACCACTAGCCTGCTCGGGCGCCTTATTATTCACTTATTTATTTGGACAATCCTTAAACATTTATACTCAGGTAGGTTTGATTACTTTAATCGGGCTCATTAGCAAACACGGTATTTTAATAGTGGAATTTGCTAATAAACTTCATAAAGATGGTGCTTCGTTGCCAGAAGCTATACAGAAATCAGCTGCATTGCGTTTACGGCCTATATTAATGACAACTGGCGCCATGGTTTTTGGCGCCATCCCTTTGGTATTATCGCATGATGCGGGTTCTGAATCCCGGCATGCCATAGGAACTGTATTGATTAGCGGGCTCGGTCTTGGAACACTATTTACCCTATTTGTTTTGCCTGCGGTTTACAACATCATCAAATCCAAACTAATTGATATGCAAAAAACAGGGGGCAAAAAACGGTGCAGCAAAGAATAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Legionella pneumophila str. Paris", "NCBI_taxonomy_id": "297246", "NCBI_taxonomy_cvterm_id": "41208"}, "protein_sequence": {"accession": "CAH14033.1", "sequence": "MKLTSYFIKHPVITIILNAMIVVLGLLCLYNLSVREYPDINFPTITVSASYPNASPDLVETAITNVLEDRLAGIEGLETITSQSSAGYAQITLMFRSGTSMDRALSTTQDAVGVAKALLPPEVRSPTVERQRKSNGLPFIGISLESTSKDFGELTHYANLNLKNVFRSVQGVASVEVWGQPYTYNITLQPEKLFSFGVNVDEIVNALAKNRISLPAGNYRNKIPSTLNSELKTREDYENLLIKANSKHPILLKSLANVALETDNSQMRVRVNGHAGVVLSINKANEANPIEVSKEIRKVIKGLQQGLPKDLKINTIIDQSDFINASIKNIRSAIGEAIFLVLIIVFLFLRNIKATIIPLITIPISLLGSLLFLKLFGFSINLMTLLAMVLAIGLVVDDAIIVLENIWRHIESGLSPLDAALKGAREIGFAIIAMTFTLSSVYLPIAFIQGMLGQLFVEFAVALAGSVFISGIVALTLSPLMCANLLSASSKNWWPQFDNALEKLTKHYSNILQFILKHQKITLLTALISVVACFGFYNLISHETAPKEDRGLIGIYIPPVAGEDIGMLDNKTGKLEKKLDAIPEANNRLTFIGDWGGSIVLPLKPHAQRHRSANQIVEKLRPSFNHFPSMDPHVWSWDTGLPGVDDAGSGSELTLVISTPDHFRQLFDETEKLKSVLDKSKLFAAVNYDLRLDTMGYNIDLDYNQLAKLGLTANQVAKTIEVFFSGDKSQTFEKDGVVYNISIKGDSSPWTLNELYLTTNEGKSVSLGAITKMQPKAQPATLDHYQQMRSTTLHVQLHKGDSMAKAIEKLWGTTKEVMPQHYKLTWIGAAKAFHESSNSMLFLFFLSLAFIYAILCTQFENFTDPFIILFTVPLACSGALLFTYLFGQSLNIYTQVGLITLIGLISKHGILIVEFANKLHKDGASLPEAIQKSAALRLRPILMTTGAMVFGAIPLVLSHDAGSESRHAIGTVLISGLGLGTLFTLFVLPAVYNIIKSKLIDMQKTGGKKRCSKE"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "LpeB", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41209", "model_name": "LpeB", "model_type_id": "40292"}, "2770": {"model_id": "2770", "ARO_accession": "3004102", "model_param": {"blastp_bit_score": {"param_value": "400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Methyltransferase enzyme first described in Streptoalloteichus tenebrarius. Confers resistance to aminoglycoside antibiotics (esp. apramycin) through methylation of the 16S rRNA at A1408, thereby modifying the antibiotic target.", "model_sequences": {"sequence": {"4082": {"dna_sequence": {"fmax": "748", "fmin": "100", "accession": "NG_050561.1", "strand": "+", "sequence": "ATGCGCCGCGTGGTGGGCAAGCGGGTCCAGGAGTTCTCCGACGCCGAGTTCGAGCAGCTACGGAGTCAGTACGACGACGTGGTGCTCGACGTCGGCACCGGCGACGGGAAGCATCCGTACAAGGTCGCCCGCCAGAACCCCTCCCGGCTGGTGGTGGCGCTCGACGCCGACAAGAGCCGGATGGAGAAGATCTCGGCGAAGGCGGCGGCCAAGCCCGCGAAGGGCGGCCTGCCCAACCTGCTGTACCTGTGGGCCACCGCCGAGCGGCTCCCCCCGTTGTCGGGGGTGGGCGAGCTGCACGTCCTCATGCCGTGGGGCAGCCTGCTGCGCGGGGTCCTCGGCTCCTCGCCGGAGATGCTGCGCGGGATGGCGGCGGTGTGCCGGCCGGGCGCGTCCTTCCTGGTCGCGCTGAACCTGCACGCCTGGCGGCCCTCGGTGCCGGAGGTGGGCGAGCACCCCGAGCCCACCCCGGACTCCGCCGACGAGTGGCTGGCGCCCCGCTACGCCGAGGCCGGGTGGAAGCTCGCCGACTGCCGCTACCTGGAGCCGGAGGAGGTGGCGGGTCTGGAGACCTCCTGGACCCGCCGTCTGCACTCCTCCCGCGACCGGTTCGACGTGCTCGCGCTCACCGGCACGATCAGTCCGTGA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Streptoalloteichus tenebrarius", "NCBI_taxonomy_id": "1933", "NCBI_taxonomy_cvterm_id": "41214"}, "protein_sequence": {"accession": "WP_063964000.1", "sequence": "MRRVVGKRVQEFSDAEFEQLRSQYDDVVLDVGTGDGKHPYKVARQNPSRLVVALDADKSRMEKISAKAAAKPAKGGLPNLLYLWATAERLPPLSGVGELHVLMPWGSLLRGVLGSSPEMLRGMAAVCRPGASFLVALNLHAWRPSVPEVGEHPEPTPDSADEWLAPRYAEAGWKLADCRYLEPEEVAGLETSWTRRLHSSRDRFDVLALTGTISP"}}}}, "ARO_category": {"36658": {"category_aro_name": "antibiotic target modifying enzyme", "category_aro_cvterm_id": "36658", "category_aro_accession": "3000519", "category_aro_description": "Enzymes that confer resistance by modifying antibiotic targets."}, "36243": {"category_aro_name": "determinant of aminoglycoside resistance", "category_aro_cvterm_id": "36243", "category_aro_accession": "3000104", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to aminoglycoside antibiotics."}}, "ARO_name": "kamB", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41213", "model_name": "kamB", "model_type_id": "40292"}, "2771": {"model_id": "2771", "ARO_accession": "3004103", "model_param": {"blastp_bit_score": {"param_value": "850", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "QepA2 is a plasmid-mediated quinolone resistance pump found in an Escherichia coli isolate from France", "model_sequences": {"sequence": {"4083": {"dna_sequence": {"fmax": "1636", "fmin": "100", "accession": "NG_050460.1", "strand": "+", "sequence": "ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTCTTCGCATTCGGCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGATCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGCGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCCGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGGTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCATGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGGCGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "WP_032492277.1", "sequence": "MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAAFFAFGSVLAALADTAALLIAARALLGLAGATIAPSTMALIRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGAGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHAPFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPWSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVMGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQAAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "QepA2", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41215", "model_name": "QepA2", "model_type_id": "40292"}, "2773": {"model_id": "2773", "ARO_accession": "3004105", "model_param": {"blastp_bit_score": {"param_value": "350", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "TMB-1 is a TMB metallo-beta-lactamase found in Achromobacter sp.", "model_sequences": {"sequence": {"4085": {"dna_sequence": {"fmax": "753", "fmin": "15", "accession": "NG_050313", "strand": "+", "sequence": "ATGCGACCATTTTTATTTTTAATAATTTTTATCAGTCATTTCGCTTTTGCCAACGAAGAAATACCCGGATTGGAAGTTGAGGAAATTGACAACGGCGTTTTTTTGCACAAGTCATACAGCCGGGTGGAAGGCTGGGGCCTGGTAAGTTCAAACGGACTTGTTGTCATCAGCGGCGGAAAAGCATTCATTATTGACACTCCATGGTCGGAATCAGATACAGAAAAGCTTGTAGATTGGATACGATCAAAAAAGTATGAGCTGGCGGGAAGCATTTCTACACATTCACACGAAGACAAGACTGCCGGTATAAAATGGCTAAACGGCAAATCCATTACTACATATGCCTCAGCGCTGACTAATGAAATTCTAAAAAGAGAGGGTAAGGAGCAGGCAAGGAGCTCATTCAAAGGTAATGAATTTTCGCTGATGGACGGTTTTCTAGAAGTCTATTATCCCGGAGGCGGCCATACTATTGATAACTTAGTGGTATGGATCCCTAGTTCAAAAATATTGTATGGCGGCTGTTTCATACGTAGCTTGGAATCCAGTGGGCTAGGTTACACTGGTGAAGCTAAAATTGATCAGTGGCCACAATCCGCTAGAAATACAATTTCGAAGTATCCTGAAGCTAAGATTGTGGTGCCTGGTCATGGAAAAATTGGCGATTTCGAGTTGTTAAAACATACCAAGGTCCTTGCAGAAAAGGCCTCTAACAAGGCCAATCACGGCGACCGCTGA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Proteobacteria", "NCBI_taxonomy_id": "1224", "NCBI_taxonomy_cvterm_id": "40546"}, "protein_sequence": {"accession": "WP_063865147.1", "sequence": "MRPFLFLIIFISHFAFANEEIPGLEVEEIDNGVFLHKSYSRVEGWGLVSSNGLVVISGGKAFIIDTPWSESDTEKLVDWIRSKKYELAGSISTHSHEDKTAGIKWLNGKSITTYASALTNEILKREGKEQARSSFKGNEFSLMDGFLEVYYPGGGHTIDNLVVWIPSSKILYGGCFIRSLESSGLGYTGEAKIDQWPQSARNTISKYPEAKIVVPGHGKIGDFELLKHTKVLAEKASNKANHGDR"}}}}, "ARO_category": {"36696": {"category_aro_name": "antibiotic inactivation enzyme", "category_aro_cvterm_id": "36696", "category_aro_accession": "3000557", "category_aro_description": "Enzyme that catalyzes the inactivation of an antibiotic resulting in resistance.  Inactivation includes chemical modification, destruction, etc."}, "36268": {"category_aro_name": "determinant of beta-lactam resistance", "category_aro_cvterm_id": "36268", "category_aro_accession": "3000129", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to beta-lactam antibiotics."}}, "ARO_name": "TMB-1", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41217", "model_name": "TMB-1", "model_type_id": "40292"}, "2774": {"model_id": "2774", "ARO_accession": "3004106", "model_param": {"blastp_bit_score": {"param_value": "350", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "TMB-2 is a TMB metallo-beta-lactamase found in Acinetobacter sp.", "model_sequences": {"sequence": {"4086": {"dna_sequence": {"fmax": "836", "fmin": "98", "accession": "AB758278", "strand": "+", "sequence": "ATGCGACCATTTTTATTTTTAATAATTTTTATCAGTCATTTCGCTTTTGCCAACGAAGAAATACCCGGATTGGAAGTTGAGGAAATTGACAACGGCGTTTTTTTGCACAAGTCATACAGCCGGGTGGAAGGCTGGGGCCTGGTAAGTTCAAACGGACTTGTTGTCATCAGCGGCGGAAAAGCATTCATTATTGACACTCCATGGTCGGAATCAGATACAGAAAAGCTTGTAGATTGGATACGATCAAAAAAGTATGAGCTGGCGGGAAGCATTTCTACACATTCACACGAAGACAAGACTGCCGGTATAAAATGGCTAAACGGCAAATCCATTACTACATATGCCTCAGCGCTGACTAATGAAATTCTAAAAAGAGAGGGTAAGGAGCAGGCAAGGAGCTCATTCAAAGGTAATGAATTTTCGCTGATGGACGGTTTTCTAGAAGTCTATTATCCCGGAGGCGGCCATACTATTGATAACTTAGTGGTATGGATCCCTAGTTCAAAAATATTGTATGGCGGCTGTTTCATACGTAGCTTGGAACCCAGTGGGCTAGGTTACACTGGTGAAGCTAAAATTGATCAGTGGCCACAATCCGCTAGAAATACAATTTCGAAGTATCCTGAAGCTAAGATTGTGGTGCCTGGTCATGGAAAAATTGGCGATTTCGAGTTGTTAAAACATACCAAGGTCCTTGCAGAAAAGGCCTCTAACAAGGCCAATCACGGCGACCGCTGA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter courvalinii", "NCBI_taxonomy_id": "280147", "NCBI_taxonomy_cvterm_id": "41219"}, "protein_sequence": {"accession": "BAM73613.1", "sequence": "MRPFLFLIIFISHFAFANEEIPGLEVEEIDNGVFLHKSYSRVEGWGLVSSNGLVVISGGKAFIIDTPWSESDTEKLVDWIRSKKYELAGSISTHSHEDKTAGIKWLNGKSITTYASALTNEILKREGKEQARSSFKGNEFSLMDGFLEVYYPGGGHTIDNLVVWIPSSKILYGGCFIRSLEPSGLGYTGEAKIDQWPQSARNTISKYPEAKIVVPGHGKIGDFELLKHTKVLAEKASNKANHGDR"}}}}, "ARO_category": {"36696": {"category_aro_name": "antibiotic inactivation enzyme", "category_aro_cvterm_id": "36696", "category_aro_accession": "3000557", "category_aro_description": "Enzyme that catalyzes the inactivation of an antibiotic resulting in resistance.  Inactivation includes chemical modification, destruction, etc."}, "36268": {"category_aro_name": "determinant of beta-lactam resistance", "category_aro_cvterm_id": "36268", "category_aro_accession": "3000129", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to beta-lactam antibiotics."}}, "ARO_name": "TMB-2", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41218", "model_name": "TMB-2", "model_type_id": "40292"}, "2775": {"model_id": "2775", "ARO_accession": "3004107", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "SoxR is a redox-sensitive transcriptional activator that induces expression of a small regulon that includes the RND efflux pump-encoding operon mexGHI-opmD. SoxR was shown to be activated by pyocyanin.", "model_sequences": {"sequence": {"4087": {"dna_sequence": {"fmax": "2503895", "fmin": "2503424", "accession": "NC_002516.2", "strand": "-", "sequence": "CTAGCCGTCGTGCTCGCGGCCCTCGGCGTCCAGCCAGTGCGCTCCCGGCCCCTCGGCGGAAAGCTGGTCGCCGGGGTTGCGCAACGGGCAGGCCTGGAGCGACAGGCAGCCGCAACCGATGCAGCCGTCCAGTTGGTCGCGCAACAGCAGCAGCTTGTCGATGCGCTCGGTGAGATCCTCCTTCCACTGCGCCGACAGGCGCGCCCAGTCCGCCGCGCTAGGGCTGCGCCCCGCCGGCAGGGTCTGCAGGGCGCGAGCGATCTCCGCGAGGGGAATGCCGACCCGCTGGGCGACCTTGATCACCACCACCCGGCGTAGCGTCTCGCGACTGAAGCGCCGCTGGTTGCCGGCGTTGCGCTGGCTGCTGATCAGCCCCTTGGTTTCGTAGAAATGCAGGGCGGAGACCGCCACGCCGGCACGCCTGGCCAGTTCGCCGACGCTCAGTTCACGAGATGCGCAGGAATTCTTCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa PAO1", "NCBI_taxonomy_id": "208964", "NCBI_taxonomy_cvterm_id": "36804"}, "protein_sequence": {"accession": "NP_250963.1", "sequence": "MKNSCASRELSVGELARRAGVAVSALHFYETKGLISSQRNAGNQRRFSRETLRRVVVIKVAQRVGIPLAEIARALQTLPAGRSPSAADWARLSAQWKEDLTERIDKLLLLRDQLDGCIGCGCLSLQACPLRNPGDQLSAEGPGAHWLDAEGREHDG"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "35950": {"category_aro_name": "antibiotic resistant gene variant or mutant", "category_aro_cvterm_id": "35950", "category_aro_accession": "0000031", "category_aro_description": "Resistance to antibiotics is often conferred by single nucleotide polymorphisms (SNPs) and other mutations in target genes."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}, "ARO_name": "Pseudomonas aeruginosa soxR", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41228", "model_name": "Pseudomonas aeruginosa soxR", "model_type_id": "40292"}, "2776": {"model_id": "2776", "ARO_accession": "3004109", "model_param": {"blastp_bit_score": {"param_value": "525", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "rob is a positive regulator for the acrAB efflux genes, and is structurally similar to SoxS and MarA.", "model_sequences": {"sequence": {"4088": {"dna_sequence": {"fmax": "4635310", "fmin": "4634440", "accession": "NC_000913.3", "strand": "-", "sequence": "TTAACGACGGATCGGAATCAGCAGTTCACAGCGTAGATTAATTGGGCGATCTCCCGCTTTGGCATCTTCTGCCGGGTAGTATCGCTCAATATCCTGACCTTTACGGCGCGTCAGGTTGAGCATTGGCATGCACGTTCCGTATACCGTCAGGATAAACTCCTGCACGCCGGTTCCCAGACCTTCATAGGTAAACATCACATATTCGCCGCCCTGCAGCATCACCGGATGCCCCGTCAGTACATAGCCATCTGCCTGATCCTGGGCTAACGCGGTGGTATAGAATACCTCTTGCTCGTCGTCTTTATCCTGACTCGGACGCGTTTCATTCAGGCCGTAGAGCACCGGCGGAATGGTCGGCGCGTTGCCGAGAAAATCGTGCCAGAACTGATAACGCATTTCATGGCGGAAATCAGAGATTTGCTCCAGCGAACAGGAGTAGCTCTGGGTAACACCAATCAGCGGCGTATCTTCCAGGGTGACAAATTTGTGCTCTGGCATAGTGAATTCACCCAGGCGTAGCGGCGGGCGAATACCAAAGGCGCTCCATTCAGGAGAACGGCGGTAAAGTGCAGGAGTCTGGGCAAACTGCTTCTTGAATGCGCGGGTAAATGTCTGTTGAGAGTCGAAGCGGTATTGCAGCGCGATGTCCAGAATCGGACGCGCAGTCAGGCGTAGTGCGACCGCCGATTTCGACAAACGACGAGCACGAATATACGCGCCAATAGCATGGCCAGTGACATCTTTAAACATTCTCTGTAAGTGCCACTTGGAATAACCTGCTTTCGCCGCTACATTGTCGAGCGACAGGGGCTGATCCAGATGACCTTCCAGCCAGATTAAAAGGTCGCGAATAATGCCGGCCTGATCCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli str. K-12 substr. MG1655", "NCBI_taxonomy_id": "511145", "NCBI_taxonomy_cvterm_id": "36849"}, "protein_sequence": {"accession": "NP_418813.1", "sequence": "MDQAGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKSAVALRLTARPILDIALQYRFDSQQTFTRAFKKQFAQTPALYRRSPEWSAFGIRPPLRLGEFTMPEHKFVTLEDTPLIGVTQSYSCSLEQISDFRHEMRYQFWHDFLGNAPTIPPVLYGLNETRPSQDKDDEQEVFYTTALAQDQADGYVLTGHPVMLQGGEYVMFTYEGLGTGVQEFILTVYGTCMPMLNLTRRKGQDIERYYPAEDAKAGDRPINLRCELLIPIRR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}, "ARO_name": "Escherichia coli rob", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41230", "model_name": "Escherichia coli rob", "model_type_id": "40292"}, "250": {"model_id": "250", "ARO_accession": "3002701", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmr is a plasmid-encoded chloramphenicol exporter that is found in Rhodococcus fascians and Corynebacterium glutamicum", "model_sequences": {"sequence": {"663": {"dna_sequence": {"fmax": "2168", "fmin": "992", "accession": "Z12001", "strand": "+", "sequence": "GTGCCATTCGCCATCTATGTCCTGGGTATTGCTGTATTCGCCCAGGGCACATCGGAATTCATGCTGTCCGGACTCATACCGGATATGGCTCAGGATCTACAGGTTTCGGTCCCCACTGCAGGACTTCTCACTTCGGCATTCGCAATCGGCATGATCATCGGTGCCCCGTTGATGGCAATTGTCAGTATGCGGTGGCAACGTCGACGAGCGCTCTTGACCTTCCTCATCACTTTTATGGTTGTGCATGTCATCGGCGCACTCACCGACAGTTTCGGCGTCTTGCTGGTCACCCGGATCGTAGGAGCACTGGCCAACGCCGGTTTCCTGGCTGTAGCGCTGGGCGCAGCCATGTCGATGGTTCCTGCCGACATGAAGGGACGAGCGACCTCAGTTCTACTGGGCGGAGTGACCATCGCCTGCGTAGTTGGAGTCCCGGGCGGAGCGCTATTGGGCGAACTGTGGGGATGGCGCGCCTCGTTCTGGGAGGTAGTGCTGATTTCCGCACCGGCAGTGGCAGCGATCATGGCATCGACCCCTGCTGATTCCCCTACAGATTCTGTTCCGAACGCGACCCGCGAACTGTCCTCGCTGCGTCAACGCAAACTTCAACTGATCTTGGTGCTGGGCGCGCTGATCAACGGTGCCACCTTCTGTTCCTTCACCTACCTGGCTCCGACGCTCACCGACGTCGCCGGGTTCGACTCTCGCTGGATCCCTTTGCTTCTCGGACTGTTCGGACTGGGGTCGTTCATCGGCGTCAGTGTCGGTGGCCGGCTCGCTGACACCCGTCCGTTTCAATTGCTGGTGGCGGGCTCGGCAGCTCTTCTGGTCGGGTGGATCGTGTTCGCTATCACTGCCTCTCACCCGGTAGTGACCCTGGTGATGCTGTTCGTGCAAGGAACGCTGTCGTTCGCTGTGGGGTCGACGTTGATCTCGCGAGTGCTCTACGTCGCCGACGGTGCTCCGACTTTGGGGGGATCCTTCGCTACGGCTGCCTTCAATGTCGGAGCCGCATTGGGGCCGGCCCTCGGCGGTGTGGCCATCGGTATCGGAATGGGCTATCGCGCTCCACTGTGGACCAGCGCGGCTCTGGTGGCACTTGCGATCGTGATCGGTGCCGCGACGTGGACGCGTTGGCGGGAACCACGTCCAGCGCTGGACACCGTTCCTCCGTGAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Rhodococcus fascians", "NCBI_taxonomy_id": "1828", "NCBI_taxonomy_cvterm_id": "39552"}, "protein_sequence": {"accession": "CAA78046.1", "sequence": "MPFAIYVLGIAVFAQGTSEFMLSGLIPDMAQDLQVSVPTAGLLTSAFAIGMIIGAPLMAIVSMRWQRRRALLTFLITFMVVHVIGALTDSFGVLLVTRIVGALANAGFLAVALGAAMSMVPADMKGRATSVLLGGVTIACVVGVPGGALLGELWGWRASFWEVVLISAPAVAAIMASTPADSPTDSVPNATRELSSLRQRKLQLILVLGALINGATFCSFTYLAPTLTDVAGFDSRWIPLLLGLFGLGSFIGVSVGGRLADTRPFQLLVAGSAALLVGWIVFAITASHPVVTLVMLFVQGTLSFAVGSTLISRVLYVADGAPTLGGSFATAAFNVGAALGPALGGVAIGIGMGYRAPLWTSAALVALAIVIGAATWTRWREPRPALDTVPP"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmr", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39135", "model_name": "cmr", "model_type_id": "40292"}, "138": {"model_id": "138", "ARO_accession": "3002690", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cml is a plasmid or chromosome-encoded chloramphenicol resistance determinant (putative transmembrane protein) that is found in Escherichia coli and Streptomyces lividans", "model_sequences": {"sequence": {"755": {"dna_sequence": {"fmax": "1686", "fmin": "507", "accession": "X59968", "strand": "+", "sequence": "ATGCCTCTTCCGCTGTACCTGCTCGCCGTGGCCGTCTGCGCCATGGGCACCTCGGAGTTCATGCTCGCCGGTCTCGTGCCGGACATCGCCTCGGATCTCGGCGTCACCGTCGGGACCGCAGGCACGCTCACCTCCGCCTTCGCGACCGGCATGATCGTCGGCGCTCCCCTCGTGGCGGCGCTGGCCCGCACCTGGCCCAGGCGTTCCAGCCTCCTCGGATTCATCCTCGCCTTCGCGGCGGCACACGCCGTGGGAGCCGGCACCACGAGCTTCCCCGTCCTGGTGGCCTGCCGGGTCGTGGCCGCGCTCGCGAACGCGGGATTCCTCGCGGTCGCACTGACGACTGCCGCCGCACTGGTCCCTGCCGACAAGCAGGGACGCGCGCTGGCCGTGCTGCTGTCCGGCACGACGGTGGCCACGGTCGCCGGCGTCCCCGGCGGGTCACTCCTCGGCACGTGGCTCGGCTGGCGGGCCACGTTCTGGGCCGTCGCCGTCTGCTGCCTGCCCGCGGCGTTCGGCGTGCTGAAGGCAATCCCCGCCGGACGTGCGACGGCAGCGGCGACCGGTGGGCCGCCGCTGCGAGTCGAGCTCGCCGCGCTCAAGACCCCCCGGTTGCTGCTGGCGATGCTGCTGGGCGCGCTGGTGAACGCGGCAACCTTCGCGAGCTTCACCTTCCTGGCCCCCGTCGTGACCGACACCGCAGGGCTGGGCGACCTGTGGATCTCTGTCGCCCTGGTGCTCTTCGGCGCCGGTTCCTTCGCCGGCGTCACCGTCGCCGGACGACTGTCCGACCGACGCCCCGCCCAGGTGCTCGCCGTCGCCGGTCCGCTGCTGCTCGTCGGCTGGCCCGCGCTGGCGATGCTGGCCGACCGGCCGGTCGCCCTGCTGACCCTCGTGTTCGTCCAAGGCGCACTGTCGTTCGCGCTGGGCAGCACGCTGATCACGCGGGTCCTCTACGAGGCGGCGGGAGCACCCACCATGGCCGGTTCGTACGCGACCGCCGCCCTCAACGTGGGCGCCGCGGCCGGACCGCTCGTCGCCGCGACCACTCTCGGCCACACGACCGGCAACCTCGGGCCGCTGTGGGCGAGCGGGCTCCTGGTCGCCGTCGCGCTGCTCGTCGCGTTCCCCTTCCGCACGGTGATCACGACGGCCGCACCCGCCGACGCGACCCGGTGAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Streptomyces lividans 1326", "NCBI_taxonomy_id": "1200984", "NCBI_taxonomy_cvterm_id": "39551"}, "protein_sequence": {"accession": "CAA42594.1", "sequence": "MPLPLYLLAVAVCAMGTSEFMLAGLVPDIASDLGVTVGTAGTLTSAFATGMIVGAPLVAALARTWPRRSSLLGFILAFAAAHAVGAGTTSFPVLVACRVVAALANAGFLAVALTTAAALVPADKQGRALAVLLSGTTVATVAGVPGGSLLGTWLGWRATFWAVAVCCLPAAFGVLKAIPAGRATAAATGGPPLRVELAALKTPRLLLAMLLGALVNAATFASFTFLAPVVTDTAGLGDLWISVALVLFGAGSFAGVTVAGRLSDRRPAQVLAVAGPLLLVGWPALAMLADRPVALLTLVFVQGALSFALGSTLITRVLYEAAGAPTMAGSYATAALNVGAAAGPLVAATTLGHTTGNLGPLWASGLLVAVALLVAFPFRTVITTAAPADATR"}}}}, "ARO_category": {"36191": {"category_aro_name": "determinant of phenicol resistance", "category_aro_cvterm_id": "36191", "category_aro_accession": "3000052", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to phenicol (chloramphenicol) antibiotics. These include chloramphenicol acetyltransferase (CAT) enzymes, which are found in a large number of species."}}, "ARO_name": "Streptomyces lividans cml", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39124", "model_name": "cml", "model_type_id": "40292"}, "2800": {"model_id": "2800", "ARO_accession": "3004146", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Acfr-like 23S rRNA methyltransferase shown to confer resistance to linezolid and phenicol antibiotics, including florfenicol and chloramphenicol, in Clostridium.", "model_sequences": {"sequence": {"4138": {"dna_sequence": {"fmax": "3036527", "fmin": "3035492", "accession": "NC_009495.1", "strand": "-", "sequence": "TCATAATTCATTTTCATAACACAATTGTCCGCAAGCAGCACTAATTTCAGAACCAAATTGTGTTCTAACAGTTGCACTAATACTAGCTTTCTTTAGTGTACTGCAAAATTGCTTGATAGCACTTGAAGATTGAAATTTAAAAGTTGTTTTGTCCGTAGAATTATAAGGTATCAAATCAATGTGATATAAATGCTCCCATGAACCACGATTTCTCAATAAACCTATAATTGCCTCTGCATGTTCTTTCGAATCATTAATTCCTTCAAGCATAATATAAGCAATAAACACTCGTCGTCCCGTATGAATGATATGTTCATCTAATGTCTTCATTACCTCATTCAATGGAAATCTTTTATTTATAGGCATTAAATCGCTTCGTTGACTTTCAAATGGTGAATGAAGTGAAAAAGCCAGATTCACTTGTGGAAATTCTTTAGTCAGTCTTTGAATTCCTGGTATAATGCCAATTGTTGAAATAGTAATTCTTCGTTGACTTAACCCAAATAAATTTTGATCAGTTAAAATTTTTACTGCATCAAATAACTCTGGATTTGCAAAAGCCTCACCCATTCCCATAAATGAAATACTATTCAATCTATGGTCATTAAAATAGAAATAAAGTAATTGGTCAGTTATCTCATCAGCAGTAAGATTGCGTTTAAATCCAGCACTTCCCGTTGCACAAAAACGACATCCAAAACTACAACCACATTGGGAAGAAATACAAAACGATTCCCACCCCTGTTTATACTTTAGTCCAACGGCTTCTATTCTTTCTCCATCAGTCAATTCAAATAACAACTTTTGAGCTTGTTTAGAATCTTGTGAAAAAATAGGTGTTACACTAGATACATTCTTTCCAAACTCATTTACTAAAGCTATCCTTAACGCTTTTGGTAGTATATGCATATCATGAAAATTATCTATTCTTTGATGAAAAATAGCTTTTGTAAGCTGTTCGTATCTATAATCAGGTAATTTTAAATTCGATGCTATTTGTTTCATTTTTCCATATTTCGTTTTTGTCTGTTTCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridium botulinum A str. ATCC 3502", "NCBI_taxonomy_id": "413999", "NCBI_taxonomy_cvterm_id": "41276"}, "protein_sequence": {"accession": "YP_001255356.1", "sequence": "MKQTKTKYGKMKQIASNLKLPDYRYEQLTKAIFHQRIDNFHDMHILPKALRIALVNEFGKNVSSVTPIFSQDSKQAQKLLFELTDGERIEAVGLKYKQGWESFCISSQCGCSFGCRFCATGSAGFKRNLTADEITDQLLYFYFNDHRLNSISFMGMGEAFANPELFDAVKILTDQNLFGLSQRRITISTIGIIPGIQRLTKEFPQVNLAFSLHSPFESQRSDLMPINKRFPLNEVMKTLDEHIIHTGRRVFIAYIMLEGINDSKEHAEAIIGLLRNRGSWEHLYHIDLIPYNSTDKTTFKFQSSSAIKQFCSTLKKASISATVRTQFGSEISAACGQLCYENEL"}}}}, "ARO_category": {"36406": {"category_aro_name": "determinant of linezolid resistance", "category_aro_cvterm_id": "36406", "category_aro_accession": "3000267", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to linezolid antibiotics."}, "36454": {"category_aro_name": "determinant of macrolide resistance", "category_aro_cvterm_id": "36454", "category_aro_accession": "3000315", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to macrolide antibiotics."}, "36658": {"category_aro_name": "antibiotic target modifying enzyme", "category_aro_cvterm_id": "36658", "category_aro_accession": "3000519", "category_aro_description": "Enzymes that confer resistance by modifying antibiotic targets."}, "36191": {"category_aro_name": "determinant of phenicol resistance", "category_aro_cvterm_id": "36191", "category_aro_accession": "3000052", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to phenicol (chloramphenicol) antibiotics. These include chloramphenicol acetyltransferase (CAT) enzymes, which are found in a large number of species."}, "36380": {"category_aro_name": "determinant of lincosamide resistance", "category_aro_cvterm_id": "36380", "category_aro_accession": "3000241", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to lincosamide antibiotics."}, "36379": {"category_aro_name": "determinant of streptogramin resistance", "category_aro_cvterm_id": "36379", "category_aro_accession": "3000240", "category_aro_description": "Ezymes, other proteins or other gene products shown clinically to confer resistance to streptogramin antibiotics."}}, "ARO_name": "cfrC", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41275", "model_name": "cfrC", "model_type_id": "40292"}, "2785": {"model_id": "2785", "ARO_accession": "3004122", "model_param": {"blastp_bit_score": {"param_value": "650", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36, which did not allow penetration by certain \u03b2-lactams. Also, when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.", "model_sequences": {"sequence": {"4099": {"dna_sequence": {"fmax": "1463", "fmin": "0", "accession": "AJ011502", "strand": "+", "sequence": "TTTTACCGATAAACAACATCATTCCGCAGAATGAGACGGCAACAATAAATTATTGGCATGACAATAAAGGCATATAACGCGCAAATAATACGTGATTAGCCCGGGCATGTATAATTTTTATTTTGTATATTATCTATAAATGCATTCAGCATAATTATCACCATTTCATTGGTATTATTTATTTTAGATTTTACTTATATCGTAACAATTGAGTCTTACCGGATCTCAGACCGCTCCTTTAGCATGAGTTCACTTCCCACCCGGAAGTTAAAACATAAAAACAGTTAAAGGAATTTCTTCATGAAAAGAAAAGTACTGGCCCTCGTTATTCCGGCTTTATTAGCCGCCGGTGCCGCGCATGCGGCGGAAATTTATAATAAAGACGGGAATAAATTAGATCTCTATGGCAAGGTAGATGGTCTGCATTATTTCTCCAGCGACTCGAAAAAAGACGGCGATCAAACTTATTTACGTTTTGGCTTTAAAGGCGAAACCCAGATCAACGATATTCTTACCGGCTATGGCCAGTGGGAATATAACGTTCAGGCCAACAACACCGAGACCTCCAGCGATCAGGCGTGGACCCGTCTGGCATTCGCCGGTATCAAAGTGGGCGATTACGGCTCCTTCGACTACGGTCGTAACTACGGCGTGCTGTACGACGTTGAAGGCTGGACCGATATTCTGCCGGAGTTCGGCGGCGACTCCTACACCTATGCGGATAACTTTATGGCAGGCCGCGCCAACGGCGTCGCAACCTACCGCAACAGCGATTTTTTCGGTCTGGTGGAGGGTCTGAACTTCGCCCTGCAGTATCAGGGTAAAAACGAAGGCCAGAACGCGCAGGATATCAACGTCGGCACCAATAACCGCAGCAGCGACAGCGATGTTCGCTTCGACAATGGCGATGGTTTCGGCCTCTCTACTTCCTACGACTTCGGCATGGGCATCAGCGCGGCGGCAGCTTACACCTCGTCTGACCGTACTAACGATCAGATGACCCAGACCAACGCGCGCGGCGATAAAGCGGAAGCCTGGACCGCCGGCCTGAAGTACGACGCCAACGATATCTACCTGGCGACCATGTACTCTGAAACCCGCAATATGACCCCGTACGGCAATGACGGCGTGGCCAATAAAACACAAAACTTCGAAGTCACCGCGCAGTATCAGTTCGACTTCGGCCTGCGTCCGGCCATCTCCTACCTGCAGTCCAAAGGCAAAGATCTGTACAATAACGGCCGCTATGCCGATAAAGATCTGGTCAAATATATGGACGTTGGCGCGACCTATTACTTCAACCGTAATATGTCCACCTATGTTGATTACAAAATCAACCTGCTGGATGGTAACGACAAATTCTACGAAGACAACGGTATCTCTACCGATAACATCGTCGCCCTGGGCCTGGTTTACCAGTTCTGATGCGCCTGCCCGCCGGTTCCGGCGGGCTTTCCCCCACC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "CAA09666", "sequence": "MKRKVLALVIPALLAAGAAHAAEIYNKDGNKLDLYGKVDGLHYFSSDSKKDGDQTYLRFGFKGETQINDILTGYGQWEYNVQANNTETSSDQAWTRLAFAGIKVGDYGSFDYGRNYGVLYDVEGWTDILPEFGGDSYTYADNFMAGRANGVATYRNSDFFGLVEGLNFALQYQGKNEGQNAQDINVGTNNRSSDSDVRFDNGDGFGLSTSYDFGMGISAAAAYTSSDRTNDQMTQTNARGDKAEAWTAGLKYDANDIYLATMYSETRNMTPYGNDGVANKTQNFEVTAQYQFDFGLRPAISYLQSKGKDLYNNGRYADKDLVKYMDVGATYYFNRNMSTYVDYKINLLDGNDKFYEDNGISTDNIVALGLVYQF"}}}}, "ARO_category": {"36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Klebsiella pneumoniae OmpK37", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41247", "model_name": "Klebsiella pneumoniae OmpK37", "model_type_id": "40292"}, "2787": {"model_id": "2787", "ARO_accession": "3004124", "ARO_description": "The outer membrane protein M35 of Moraxella catarrhalis is an antigenically conserved porin. Down-regulation of M35 significantly increases the MICs of aminopenicillins, specifically amoxicillin.", "model_sequences": {"sequence": {"4101": {"dna_sequence": {"fmax": "1077", "fmin": "0", "accession": "AY905613", "strand": "+", "sequence": "ATGAAAAAACTTGCTCTAGCAACCGCTGTCGCTGCTTTATCTGTATCTGCTGCACAAGCAACACCGACTGTTTACGGTAAAGCGTTTTTAACTGTTGATGCCAACAATACTGATACAACTTATAATTCAGGTCTTGTACAATTATCTGAAGATACCAATGAAAGCGGGCTTAACTCAAATACCTCACGCATTGGTTTTAAAGGTTCTGAAGCTTTAAATGCTAATACTGATGTTGTGTATCAACTTGAATATAAGATTGACATTGATGCTGATCGTGGCGATAACTTTAAATCTCGTGATACTTACCTAGGTCTTGCTCATAAACAATACGGCACATTGTTGGCTGGTCGCTTAACGACTATTGATGACAGTGTTGATTTTGCCAGCATGTTGGAAGATAATAATGTCGCTGACATCGGTCCTACTTTTAATGCCCCTCGTGCCAACAATGCCTTTGCTTATGTATCACCTGAGTATAATGGTACTCAGTTCTTAGCTATGTATGCATTTGACTCAGATACTGACAAGGGCGGTCTTGCCAAAGATGACCAGTTTGGTGTGGGTGCAACTTATAGCACAGGCCCTATCAATGCAGGTGCGACTTATATTCACTACGGTGATGACAGTCACATTCGCCTATCTGGCAACTATGCGGTTTCTCCAGCATTGACTGTAGGTGCTTTATATCAAATCTCAGAATTTGGTGTCGCTGCCAAAAATCAAAAAGCCAGTCCTTTGTCTGAGGGCAAGGTAGGCGATAAAAAAGAAAACACCCTTATCGTGAGTGGCGAGATGAAAACTGCCACGCCATGGACAGCCTATGGTCAGGCAACTTTGATTAAAAATGTTGCTGGTAATGATGGCGATGAGTCAGTGGGTGTTGGTATTGGTGGTAAATATGCCTTTAATAAAGCCACCACAGGTCATGTCTACACTGGCTATGTCAACAGCGAGCGTAAAAATGTCAAGTATGAGGGCAGTAATGAAACACATAAAAATGCACACAAAGATACAAAGTTTGATGGTTATAAGAACAGTGGCTTTGGTATCGGCGCAGGTTTAGAATATAAATTCTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella catarrhalis", "NCBI_taxonomy_id": "480", "NCBI_taxonomy_cvterm_id": "41250"}, "protein_sequence": {"accession": "AAX99225", "sequence": "MKKLALATAVAALSVSAAQATPTVYGKAFLTVDANNTDTTYNSGLVQLSEDTNESGLNSNTSRIGFKGSEALNANTDVVYQLEYKIDIDADRGDNFKSRDTYLGLAHKQYGTLLAGRLTTIDDSVDFASMLEDNNVADIGPTFNAPRANNAFAYVSPEYNGTQFLAMYAFDSDTDKGGLAKDDQFGVGATYSTGPINAGATYIHYGDDSHIRLSGNYAVSPALTVGALYQISEFGVAAKNQKASPLSEGKVGDKKENTLIVSGEMKTATPWTAYGQATLIKNVAGNDGDESVGVGIGGKYAFNKATTGHVYTGYVNSERKNVKYEGSNETHKNAHKDTKFDGYKNSGFGIGAGLEYKF"}}}}, "ARO_category": {"40439": {"category_aro_name": "gene conferring resistance via absence", "category_aro_cvterm_id": "40439", "category_aro_accession": "3003768", "category_aro_description": "Deletion of gene or gene product results in resistance. For example, deletion of a porin gene blocks drug from entering the cell."}, "36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Moraxella catarrhalis M35", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "41249", "model_name": "Moraxella catarrhalis M35", "model_type_id": "40354"}, "2786": {"model_id": "2786", "ARO_accession": "3004123", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Heterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence, their antimicrobial susceptibility to penicillin G, cefoxitin, ceftazidime and imipenem.", "model_sequences": {"sequence": {"4100": {"dna_sequence": {"fmax": "1122", "fmin": "0", "accession": "AY312416", "strand": "+", "sequence": "ATGAACAAGACTCTGATTGTTGCAGCAGTTGCTGCATCGTTCGCAACCGTCGCTCACGCGCAAAGCAGCGTCACGCTGTACGGTGTGCTCGACGCGGGCATCACGTACCAAAGCAACGTCGCGACGCCGTCGGGCTCGGGCAAGTCGCTGTGGTCGGTCGGCGCCGGCGTCGACCAAAGCCGTTTCGGTCTGCGCGGCTCGGAAGACCTGGGTGGCGGCCTGAAGGCGATCTTCACGTTGGAAAGCGGCTTCAACATCGGTAACGGCCGCTTCAACAACGGTGGCGGCATGTTCAACCGTCAAGCGTTCGTCGGTCTGTCGAGCAACTACGGCACCGTCACGCTGGGCCGTCAGTACGACGCAACCCAAGACTACCTGTCGCCGCTGTCGGCAACGGGCACCTGGGGCGGCACGTACTTCGCGCACCCGCTCAACAACGACCGCCTGAACACGAACGGCGACGTCGCGGTGAACAATACGGTCAAGTTCACGAGCGCGAACTACGCCGGCCTGCAATTCGGCGGCACGTACTCGTTCTCGAACAACTCGCAATTCGCGAACAACCGTGCATACAGCGCGGGCGCTTCGTACCAGTTCCAAGGCCTGAAGGTCGGTGCGGCGTACTCGCAAGCTAACAACGCTGGCGCGAATACCACGGGCGCAACGGATCCGCTGACCGGCTTCAACATCGGCGGCACGAACGCAGCAAGCATCCAAGGCCGTTCGCGCGTGTACGGCGCCGGCGCAAGCTACGCTTACGGCCCGCTGCAAGGCGGCCTGCTCTGGACGCAATCGCGTCTCGACAACCTGGCAAACGGCGCGCCGACCATCCGTGCCGACAACTACGAAGCAAACGTGAAGTACAACCTGACGCCGGCTCTGGGTCTGGGTGTTGCTTACACGTACACGAACGCGAAGGCGAACGGCGAAAGCACTCACTGGAACCAAGTTGGCGTCCAGGCCGACTACGCGCTGTCGAAGCGCACCGACGTGTACGCACAAGCCGTGTACCAGCGTTCGTCGAAGAACGCGAATGCGTCGATCTACAACGGCGACCTCAGCACGCCGTTCAGCACGTCGATCAACCAAACCGCAGCGACGGTTGGTCTGCGTCACCGCTTC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Burkholderia pseudomallei", "NCBI_taxonomy_id": "28450", "NCBI_taxonomy_cvterm_id": "36923"}, "protein_sequence": {"accession": "AAP82271", "sequence": "MNKTLIVAAVAASFATVAHAQSSVTLYGVLDAGITYQSNVATPSGSGKSLWSVGAGVDQSRFGLRGSEDLGGGLKAIFTLESGFNIGNGRFNNGGGMFNRQAFVGLSSNYGTVTLGRQYDATQDYLSPLSATGTWGGTYFAHPLNNDRLNTNGDVAVNNTVKFTSANYAGLQFGGTYSFSNNSQFANNRAYSAGASYQFQGLKVGAAYSQANNAGANTTGATDPLTGFNIGGTNAASIQGRSRVYGAGASYAYGPLQGGLLWTQSRLDNLANGAPTIRADNYEANVKYNLTPALGLGVAYTYTNAKANGESTHWNQVGVQADYALSKRTDVYAQAVYQRSSKNANASIYNGDLSTPFSTSINQTAATVGLRHRF"}}}}, "ARO_category": {"36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Burkholderia pseudomallei Omp38", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41248", "model_name": "Burkholderia pseudomallei Omp38", "model_type_id": "40292"}, "2781": {"model_id": "2781", "ARO_accession": "3004114", "ARO_description": "In the presence of antibiotic stress, there is a coupled down-regulation of the porin OmpC with the OmpF.  Mutants both lacking both OmpC and OmpF proteins are resistant to cephaloridine and cefazolin. Analyses of genes involved in the increased resistance to tetracycline suggest that the up-regulation of efflux pump genes is accompanied by a decrease of OmpF and OmpC synthesis. Homologs of OmpC have been identified in Escherichia coli, Salmonella enterica, Enterobacter aerogenes and Serratia marcescens.", "model_sequences": {"sequence": {"4096": {"dna_sequence": {"fmax": "1104", "fmin": "0", "accession": "KY086517", "strand": "+", "sequence": "ATGAAAGTTAAAGTACTGTCCCTCCTGGTCCCAGCTCTGCTGGTAGCAGGCGCAGCAAACGCTGCTGAAGTTTACAACAAAGACGGCAACAAATTAGATCTGTACGGTAAAGTAGACGGCCTGCACTATTTCTCTGACAACAAAGATGTAGATGGCGACCAGACCTACATGCGTCTTGGCTTCAAAGGTGAAACTCAGGTTACTGACCAGCTGACCGGTTACGGCCAGTGGGAATATCAGATCCAGGGCAACAGCGCTGAAAACGAAAACAACTCCTGGACCCGTGTGGCATTCGCAGGTCTGAAATTCCAGGATGTGGGTTCTTTCGACTACGGTCGTAACTACGGCGTTGTTTACGACGTAACTTCCTGGACCGACGTACTGCCAGAATTCGGTGGCGACACCTACGGTTCTGACAACTTCATGCAGCAGCGTGGTAACGGCTTTGCGACCTACCGTAACACTGACTTCTTCGGTCTGGTTGACGGCCTGAACTTTGCTGTTCAGTACCAGGGCAAAAACGGTAGCGTAAGCGGCGAAGGCATGACCAACAATGGTCGCGATGCTCTGCGTCAGAACGGCGACGGCGTTGGCGGTTCTATCACTTATGATTACGAAGGCTTCGGTATCGGTGCTGCAGTTTCCAGCTCCAAACGTACTGATGCTCAGAACACCGCTGCTTACATCGGTAACGGCGACCGTGCTGAAACCTACACCGGTGGTCTGAAATACGACGCTAACAACATCTACCTGGCTGCTCAGTACACCCAGACCTACAACGCAACTCGCGTAGGTTCCCTGGGTTGGGCGAACAAAGCACAGAACTTCGAAGCTGTTGCTCAGTACCAGTTCGACTTCGGTCTGCGTCCGTCTGTAGCATACCTGCAGTCTAAAGGTAAAAACCTGGGTGTCATCAATGGTCGTAACTACGACGACGAAGATATCCTGAAATATGTTGATGTTGGCGCGACCTACTACTTCAACAAAAACATGTCCACCTACGTTGACTACAAAATCAACCTGCTGGACGACAACCAGTTCACTCGTGACGCTGGCATCAACACTGATAACATCGTAGCTCTGGGTCTGGTTTACCAGTTCTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "APB87301", "sequence": "MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGSVSGEGMTNNGRDALRQNGDGVGGSITYDYEGFGIGAAVSSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSVAYLQSKGKNLGVINGRNYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF"}}}}, "ARO_category": {"36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "porin OmpC", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "41238", "model_name": "porin OmpC", "model_type_id": "40354"}, "2780": {"model_id": "2780", "ARO_accession": "3004113", "model_param": {"blastp_bit_score": {"param_value": "250", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "fosA7 is an enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.", "model_sequences": {"sequence": {"4093": {"dna_sequence": {"fmax": "37245", "fmin": "36822", "accession": "LAPJ01000014.1", "strand": "+", "sequence": "ATGCTTCAATCTCTGAACCACTTAACGCTTGCTGTCAGTAATTTGCAAACTAGCCTGACCTTCTGGCGCGATTTGCTGGGGTTGCAGCTACATGCTGAGTGGGATACTGGCGCTTACCTTACCTGTGGCGACCTTTGGGTCTGTCTTTCTTACGACGTATCCTGTAACTACGTGGCCCCGCAGGAATGTGACTATACCCACTACGCATTCAGCATCGCGCCAGAAGATTTTGAACCGTTCTCGTATAAGCTGAAACAGGCGGGAGTGACGGTCTGGAAAGACAATAAAAGCGAAGGGCAATCTTTCTATTTTCTTGACCCCGATGGCCACAAGCTGGAACTGCATGTGGGAGATTTAGCATCTCGACTGGCGCAGTGCCGGGAGAAGCCTTACTCTGGAATGCGTTTCGGGCCTGGAAAATAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Salmonella enterica subsp. enterica serovar Heidelberg", "NCBI_taxonomy_id": "611", "NCBI_taxonomy_cvterm_id": "35663"}, "protein_sequence": {"accession": "KKE03230.1", "sequence": "MLQSLNHLTLAVSNLQTSLTFWRDLLGLQLHAEWDTGAYLTCGDLWVCLSYDVSCNYVAPQECDYTHYAFSIAPEDFEPFSYKLKQAGVTVWKDNKSEGQSFYFLDPDGHKLELHVGDLASRLAQCREKPYSGMRFGPGK"}}}}, "ARO_category": {"36696": {"category_aro_name": "antibiotic inactivation enzyme", "category_aro_cvterm_id": "36696", "category_aro_accession": "3000557", "category_aro_description": "Enzyme that catalyzes the inactivation of an antibiotic resulting in resistance.  Inactivation includes chemical modification, destruction, etc."}, "36410": {"category_aro_name": "determinant of fosfomycin resistance", "category_aro_cvterm_id": "36410", "category_aro_accession": "3000271", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to fosfomycin antibiotics."}}, "ARO_name": "FosA7", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41234", "model_name": "FosA7", "model_type_id": "40292"}, "971": {"model_id": "971", "ARO_accession": "3002694", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlA4 is a plasmid-encoded chloramphenicol exporter that is found in Klebsiella pneumoniae", "model_sequences": {"sequence": {"656": {"dna_sequence": {"fmax": "4908", "fmin": "3648", "accession": "AF156486", "strand": "+", "sequence": "GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTGCTGGCATCACTCGGCATGGACATGTACTTGCCGGCAGTGCCTTTTATGCCAAACGCGCTTGGCACGACAGCGAGCACAGTTCAGCTTACGCTGGCAACGTACTTGGTCATGATCGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTTTTACGTCATTGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACGTTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAACGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCAGAAACCCGGGTGCAACGAGTTACGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTTCATTGCGCCCGGACTAATAATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTTGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTGCTCCGATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCACCCAATGGCGCTCTTCAAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTTTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGCGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACGTCAAATCCCAATCGTTGAG"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "AAF27726.1", "sequence": "MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTVQLTLATYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLAFTSLAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVTGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFFIAPGLIMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFIAPMWLVGIGVATAVSVAPNGALQGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRAKGSRGQGEHDVVALQSAESTSNPNR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmlA4", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39128", "model_name": "cmlA4", "model_type_id": "40292"}, "2782": {"model_id": "2782", "ARO_accession": "3004117", "ARO_description": "A ToxR-Regulated outer membrane porin. In Vibrio cholerae, ToxR controls resistance to P2 (a BPI-derived antimicrobial peptide) by regulating the production of OmpU. OmpU also confers resistance to polymyxin B sulfate.", "model_sequences": {"sequence": {"4097": {"dna_sequence": {"fmax": "1056", "fmin": "0", "accession": "KJ699300", "strand": "+", "sequence": "ATGAACAAGACTCTGATTGCTCTTGCTGTATCAGCTGCTGCAGTGGCTACTGGCGCTTACGCTGACGGAATCAACCAAAGCGGTGACAAAGCAGGTTCAACCGTTTACAGCGCGAAAGGTACTTCTCTAGAAATCGGTGGCCGTGCTGAAGCGCGCCTATCTCTGAAAGATGGCAAAGCTGAAGATAAATCTCGCGTACGCCTGAATTTCCTAGGTAAAGCAGAAATCAATGACAGCCTATACGGCATCGGTTTCTACGAAGGTGAATTCACTACTGCAGATAACGCTGACGGCTCAGAATTAGATAACCGTTACACCTACGCTGGTATCGGTGGCACTTACGGTGAAGTGACTTATGGTAAAAACGATGGTGCATTGGGCGTAATCACTGACTTCACCGATATCATGTCTTACCACGGTAACTCAGCCGCAGACAAAATCGCTGTAGCTGACCGTACAGACAACATGTTGGCTTACAAAGGCCAATTTGGTGACCTGGGCGTAAAAGCAAGCTACCGTTTTGCAGATCGTGATACTTCAACGGGTGAATTCACTGACAATAAAAAAGAAGACGGTTACTCACTATCTGCTATCTACGCCTTTGGTGACACTGGTTTCAACATCGGTGCAGGCTATGCAGATCAAAACGATAACAACGAGTACATGCTAGCCGCTTCTTACCGTATGGAAAATGTGTACTTCGGTGCTCTATTTACTGACGGTGAAAAGAATTTCAATAGTAAAAGCAACGGTAATAACTCTGTTGTGAAGGGCAAATTTACAGGTGTCCAAGATTATACTGGTTACGAATTAGCTGCTGGTTACAAGCTAGGTCAAGCTGCATTTACGACTACGTACAACAACGCAGAGACTGCAAACGATACATCAGCAAACAACGTAGCTATTGATGCTACTTACTACTTTAAGCCAAACTTCCGCACTTATATCTCTTACAACTTCAACCTACTTGACTCTGGTGACAAGCTAGGTAACAGCTCTGTATCTAAGATCGACGCTGAAGACGAACTGGCTATCGGTCTACGTTACGACTTCTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio cholerae", "NCBI_taxonomy_id": "666", "NCBI_taxonomy_cvterm_id": "36789"}, "protein_sequence": {"accession": "AID70696", "sequence": "MNKTLIALAVSAAAVATGAYADGINQSGDKAGSTVYSAKGTSLEIGGRAEARLSLKDGKAEDKSRVRLNFLGKAEINDSLYGIGFYEGEFTTADNADGSELDNRYTYAGIGGTYGEVTYGKNDGALGVITDFTDIMSYHGNSAADKIAVADRTDNMLAYKGQFGDLGVKASYRFADRDTSTGEFTDNKKEDGYSLSAIYAFGDTGFNIGAGYADQNDNNEYMLAASYRMENVYFGALFTDGEKNFNSKSNGNNSVVKGKFTGVQDYTGYELAAGYKLGQAAFTTTYNNAETANDTSANNVAIDATYYFKPNFRTYISYNFNLLDSGDKLGNSSVSKIDAEDELAIGLRYDF"}}}}, "ARO_category": {"36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Vibrio cholerae OmpU", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "41241", "model_name": "Vibrio cholerae OmpU", "model_type_id": "40354"}, "2303": {"model_id": "2303", "ARO_accession": "3003801", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Transmembrane protein which expels bicyclomycin from the cell, leading to bicyclomycin resistance. Identified in Pseudomonas aeruginosa strains responsible for outbreaks in Brazil, often appearing with blaSPM-1, another bicyclomycin resistance gene", "model_sequences": {"sequence": {"3570": {"dna_sequence": {"fmax": "5980365", "fmin": "5979156", "accession": "CP012901.1", "strand": "-", "sequence": "TCAACGGTTTCCGCCGTGCAGGGCCAAGCCCAGCGCGAGCAGGCTGCCGACGCCGCAGACGGCCATCACCAGCGCCATCGGCAGCACGCCGGGCAGCGCCAGCCAGCCGACCGCCAGGCTGGCCAGGCAGCCGAGGCCGAACTGCCCGGACACCGCCACCGCCGAAGCCGCCCCGGCCTGTCCGGGATACAACGCCAGCAGGCTGGCGATGCAGTTGGCGCCGAGCAGGCCGGTGACGCTGACGAAGCACAGCAGGCCGGGCACCAGCGCCCACAACCCGCCCCGCTCGCCGAGCGCCGCATAGCCGAGGAGGAACAGCCCGGACACGCAGGCCAGCAGGCTGCCGGCCCGCAGCAGCGGCCGCGGACCGTGGCGGCGCACCAGGCGCGCGCTGCACCAGGTGGCGAGCATCACGCCGAGGATGTTCAGGCCGAAGAACCAGCCGAAGCGCTCCGCGCGCACGCCGAAATGCTCGATGAACACGAAGGGCGCGGCGCTGATGTAGGCGAACATCCCGGCGAACGCCAGCCCCATGCACAGCACGTAGCCCAGCGCGCGACGGTCGCCGAGCAGCCGCCCATAGGCGAGAAAGGCCTGGGCCAGGCTGCCGCCGCGGCGCTCCGGCGGGTGGCTTTCGGCGACCCGCCAGACCGCCAGCAGGCAGAGCCCGGCGAACAGCGCCAGGACCACGAACAACGCGCGCCAGCCGGCCCAGAGCATCAGGTAGCCGCCGAGCAGCGGCGCGGCCAGCGGTGCCAGCATGGTCACCATGTGCATCAATGCCAGCATCCGGGCGGCCTCGCCCAACGGATAGAGGTCGCGCACCATGGCCCGCGCCAGCACCGACGCGGCGCCGCCGCCGAGGGCCTGGAGCACCCTCAGCAGGACCAGTTGCCCCGCGCTGTCGGCCAGCGCGCAGGCCAGGCTGCTGAACAGGTACAAGGCGATACCGGCCAGCAGCACCGGGCGCCGGCCGAAACGGTCGGACAAGGGGCCGTAGAACAGCATGCCGACGCAGAAGCCGACCAGGAAGCCGCTGATGCTCCGCTGCACCTGGGCATCGCTGGCGCCGAGATCGGCGGCGATCGCCGGCAGGCTCGGCAGGTACATGTCGATCGACAGCGGGCCGAACGCCACCAGCGCCGACAACAGCAGCAACAGGCGTCGTTCGCCGCTTCCGACCTGAATCCTCGATGCACTCGCAGGCAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "ALV80601.1", "sequence": "MPASASRIQVGSGERRLLLLLSALVAFGPLSIDMYLPSLPAIAADLGASDAQVQRSISGFLVGFCVGMLFYGPLSDRFGRRPVLLAGIALYLFSSLACALADSAGQLVLLRVLQALGGGAASVLARAMVRDLYPLGEAARMLALMHMVTMLAPLAAPLLGGYLMLWAGWRALFVVLALFAGLCLLAVWRVAESHPPERRGGSLAQAFLAYGRLLGDRRALGYVLCMGLAFAGMFAYISAAPFVFIEHFGVRAERFGWFFGLNILGVMLATWCSARLVRRHGPRPLLRAGSLLACVSGLFLLGYAALGERGGLWALVPGLLCFVSVTGLLGANCIASLLALYPGQAGAASAVAVSGQFGLGCLASLAVGWLALPGVLPMALVMAVCGVGSLLALGLALHGGNR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "bcr-1", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "40486", "model_name": "bcr-1", "model_type_id": "40292"}, "2789": {"model_id": "2789", "ARO_accession": "3004127", "ARO_description": "MltA-interacting protein (MipA), is an antibiotic resistance-related outer membrane protein. Deletion of mipA increases kanamycin, nalidixic acid and streptomycin resistance.", "model_sequences": {"sequence": {"4103": {"dna_sequence": {"fmax": "2468077", "fmin": "2467330", "accession": "NC_002695", "strand": "+", "sequence": "TCAGAATTTGTAGGTGATCCCGGTAGAAATCAGGCCAGTCCAGGATTTATCCACAATCGGGCTGTCAGTAACTTCATCAGACAGACGGGTGTAGCGCGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGAGTTATAGCCACGCAGACCGCTGCGAGCGGACTCTTTGCGCGATACGCCATAATAGTATTCGTTCTGGTTTTCGCTGTTCCACTGCACACCAATACCCGGAGTCACGGTCAGGCCACCGTTGGTGTAACGATACAACCAGGCCATATCCCAGACGATGCCGTTGCTGTTATCCAGGGTATCGCCAGCCAGGGTGGTACGCAGGTAACCGTACTGGGTAAAGTGAGCATAAGACAGACCAGCCATCATGGTGCTCTTACGGTCATCCAGGTGACGCATTTGGTGATCGCCACTGTCTTTAGCTTTGAAGTAAAGCGGCGACCAGTAAGCGGTAATTGAAAGTTTATCCGTTGCGTCATTCCACAGGTAGTAACCACCACCTAAGCCACGGAACCAGAAGTTATCGCCTTCATAGTTGATTACCGGTACTGGGTAAACATCGGTATCGTAATCTTTATATGGGTGTTCAACGACACCTACGCCTGCGCCCAGGGAAAATTTACCTTCAGCGTGCGCTACGCCTGCAGACGTTGCGATAAGCACTCCAAGTGCCAGAAGTTTGAGTTTGGTCAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli O157:H7 str. Sakai", "NCBI_taxonomy_id": "386585", "NCBI_taxonomy_cvterm_id": "36747"}, "protein_sequence": {"accession": "NP_310518", "sequence": "MTKLKLLALGVLIATSAGVAHAEGKFSLGAGVGVVEHPYKDYDTDVYPVPVINYEGDNFWFRGLGGGYYLWNDATDKLSITAYWSPLYFKAKDSGDHQMRHLDDRKSTMMAGLSYAHFTQYGYLRTTLAGDTLDNSNGIVWDMAWLYRYTNGGLTVTPGIGVQWNSENQNEYYYGVSRKESARSGLRGYNSNDSWSPYLELSASYNFLGDWSVYGTARYTRLSDEVTDSPIVDKSWTGLISTGITYKF"}}}}, "ARO_category": {"40439": {"category_aro_name": "gene conferring resistance via absence", "category_aro_cvterm_id": "40439", "category_aro_accession": "3003768", "category_aro_description": "Deletion of gene or gene product results in resistance. For example, deletion of a porin gene blocks drug from entering the cell."}, "36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Escherichia coli MipA", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "41253", "model_name": "Escherichia coli MipA", "model_type_id": "40354"}, "2788": {"model_id": "2788", "ARO_accession": "3004126", "model_param": {"blastp_bit_score": {"param_value": "850", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LamB is a negative regulator for antibiotic resistance, it serves as a porin to influx antibiotic. When down-regulated, it increases resistance to chlortetracycline, ciprofloxacin, balofloxacin and nalidixic acid. It also interacts with Odp1, an energy metabolic enzyme, creating a complex that decreases in antibiotic-resistant strains.", "model_sequences": {"sequence": {"4102": {"dna_sequence": {"fmax": "5102585", "fmin": "5101244", "accession": "BA000007", "strand": "+", "sequence": "ATGATGATTACTCTGCGCAAACTTCCTCTGGCGGTTGCCGTCGCAGCGGGCGTAATGTCTGCTCAGGCAATGGCTGTTGATTTCCACGGCTATGCACGTTCCGGTATTGGCTGGACAGGTAGCGGCGGTGAACAACAGTGTTTCCAGACTACCGGTGCTCAAAGTAAATACCGTCTTGGCAACGAATGTGAAACTTATGCTGAATTAAAATTGGGTCAGGAAGTGTGGAAAGAGGGCGATAAGAGCTTCTATTTCGACACTAACGTGGCCTATTCCGTCGCGCAACAGAATGACTGGGAAGCTACCGACCCGGCCTTCCGTGAAGCAAACGTGCAGGGTAAAAACCTGATCGAATGGCTGCCAGGCTCCACCATCTGGGCAGGTAAGCGCTTCTACCAACGTCATGACGTTCATATGATCGACTTCTACTACTGGGATATTTCTGGTCCTGGTGCCGGTCTGGAAAACATCGATGTTGGCTTCGGTAAACTCTCTCTGGCAGCAACCCGCTCCTCTGAAGCAGGTGGTTCTTCCTCTTTCGCCAGCAACAATATTTATGACTATACCAACGAAACCGCGAACGACGTTTTCGATGTGCGTTTAGCGCAGATGGAAGTCAACCCGGGCGGCACATTAGAACTGGGTGTCGACTACGGTCGTGCCAACCTGCGTGATAACTATCGTCTGGTTGATGGCGCATCGAAAGACGGCTGGTTATTCACTGCTGAACATACTCAGAGTGTCCTGAAGGGCTTTAACAAGTTTGTTGTTCAGTACGCTACTGACTCGATGACCTCGCAGGGTAAAGGTCTGTCGCAGGGTTCTGGCGTTGCATTTGATAACGAAAAATTTGCCTACAATATCAACAACAACGGTCACATGCTGCGTATCCTCGACCACGGTGCGATCTCCATGGGCGACAACTGGGACATGATGTACGTGGGTATGTACCAGGATATCAACTGGGATAACGACAACGGCACCAAGTGGTGGACCGTCGGTATTCGCCCGATGTACAAGTGGACGCCAATCATGAGCACCGTGATGGAAATCGGCTACGACAACGTCGAATCCCAGCGCACCGGCGACAAGAACAATCAGTACAAAATTACCCTCGCACAACAATGGCAGGCTGGCGACAGCATCTGGTCACGCCCGGCTATTCGTGTCTTCGCAACCTACGCCAAGTGGGATGAGAAATGGGGTTACGACTACAACGGCGATAGCAAGGTTAACCCGAACTACGGCAAAGCCGTTCCTGCTGATTTCAACGGCGGCAGCTTCGGTCGTGGCGACAGCGACGAGTGGACCTTCGGTGCCCAGATGGAAATCTGGTGGTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli O157:H7 str. Sakai", "NCBI_taxonomy_id": "386585", "NCBI_taxonomy_cvterm_id": "36747"}, "protein_sequence": {"accession": "BAB38442", "sequence": "MMITLRKLPLAVAVAAGVMSAQAMAVDFHGYARSGIGWTGSGGEQQCFQTTGAQSKYRLGNECETYAELKLGQEVWKEGDKSFYFDTNVAYSVAQQNDWEATDPAFREANVQGKNLIEWLPGSTIWAGKRFYQRHDVHMIDFYYWDISGPGAGLENIDVGFGKLSLAATRSSEAGGSSSFASNNIYDYTNETANDVFDVRLAQMEVNPGGTLELGVDYGRANLRDNYRLVDGASKDGWLFTAEHTQSVLKGFNKFVVQYATDSMTSQGKGLSQGSGVAFDNEKFAYNINNNGHMLRILDHGAISMGDNWDMMYVGMYQDINWDNDNGTKWWTVGIRPMYKWTPIMSTVMEIGYDNVESQRTGDKNNQYKITLAQQWQAGDSIWSRPAIRVFATYAKWDEKWGYDYNGDSKVNPNYGKAVPADFNGGSFGRGDSDEWTFGAQMEIWW"}}}}, "ARO_category": {"40439": {"category_aro_name": "gene conferring resistance via absence", "category_aro_cvterm_id": "40439", "category_aro_accession": "3003768", "category_aro_description": "Deletion of gene or gene product results in resistance. For example, deletion of a porin gene blocks drug from entering the cell."}, "36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Escherichia coli LamB", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41252", "model_name": "Escherichia coli LamB", "model_type_id": "40292"}, "1038": {"model_id": "1038", "ARO_accession": "3002699", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlB1 is a plasmid-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica", "model_sequences": {"sequence": {"731": {"dna_sequence": {"fmax": "2041", "fmin": "775", "accession": "AM296481", "strand": "+", "sequence": "GTGCGCTCTAAAGATTTTTCTTGGCGGTATTCTCTTGCCGCCACGCTATTACTGTTATCACCATTCGACTTGTTGGCATCACTCGGCATGGATATGTATCTGCCTGTGGTGCCTTTCATGGCCGGTGCACTCGGTGCCGGTGCAGGGACGATCCAGCTGACGTTGACGGTATACCTGGTTTTGCTTGGAGCCGGTCAGCTTCTCTTTGGCCCGTTATCGGATCTGCTGGGGCGCCGCCCGGTATTACTCGGTGGTGGAATTACCTATATTTTGGCTTCATTCGGACTCGCCGCAGCTTCATCACCAGAAGTTTTCCTGAGCTTCCGTATTCTTCAAGCCTGCGGTGCTTCGGCATGTCTCGTGTCCACTTTCGCGACCGTACGCGACATATATTCGGGCAGCGAGGAAAGCAACGTTATCTATGGCTTGCTCGGCTCTATGCTTGCGATGGTTCCAGCAATAGGCCCATTGTTAGGAGCGCTGGTCGACGCTTGGCTGGGGTGGCGAGCAATCTTTGGTTTGCTGGGAATCGCAATGATAGGTGCTGTTACCGCAGCTTGGCGATTCTGGCCCGAGACCCGGCGGCAGCGAACGGCAGATTTACAGTGGTCACAGCTATTGCTTCCTGTGAAATGCCTGAACTTCTGGCTGTACACCCTCTGCTACAGCGCGGGAATGGGCAGTTTCTTTGTCTTCTTCTCGACTGCCCCTTGGCTAATGATGGGCAGGCAAGCGTTATCGCAACTTAGCTTCAGCTTGCTGTTTGCGACAGTGGCCATCGCGATGATGGCTACAGCGCGGATCATGGGACGGCTGATTCCCCGATGGGGAAGCCTGAACACTTTACGAGTTGGAATGGGTTGCCTAGTGGTCGGGGCACTGTTGCTTGCTGTCGGCGAGACACTCATACCAAACTCGGTGCTTGGCTTCATCGCCCCAATGTGGCTCGTCGGTGTTGGCATTGCCACTGCGGCCTCGGTGGCACCCAATGGTGCACTTCGAGGGTTTGATCACATCGCTGGAACCGCCACAGCAGTCTACTTCTGCTTGGGTGGGTTACTGCTAGGTGGTATCGGTACTTTCATCATTGCACTTTTACCAAGTGATACCACATGGCCGATCATTGCTTATTGCCTAATCCTCGCAATAGCAGTGCTTTGTCTATCCTGCTTCAACCCCAACAGGCACCATCCCAGCGATGACGAGCATGATTCGCTTGCGACGCAAGACATCGGCCGCTCGCAATCGGGCCATGGTCATGATTAGC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bordetella bronchiseptica", "NCBI_taxonomy_id": "518", "NCBI_taxonomy_cvterm_id": "36800"}, "protein_sequence": {"accession": "CAL30186.1", "sequence": "MRSKDFSWRYSLAATLLLLSPFDLLASLGMDMYLPVVPFMAGALGAGAGTIQLTLTVYLVLLGAGQLLFGPLSDLLGRRPVLLGGGITYILASFGLAAASSPEVFLSFRILQACGASACLVSTFATVRDIYSGSEESNVIYGLLGSMLAMVPAIGPLLGALVDAWLGWRAIFGLLGIAMIGAVTAAWRFWPETRRQRTADLQWSQLLLPVKCLNFWLYTLCYSAGMGSFFVFFSTAPWLMMGRQALSQLSFSLLFATVAIAMMATARIMGRLIPRWGSLNTLRVGMGCLVVGALLLAVGETLIPNSVLGFIAPMWLVGVGIATAASVAPNGALRGFDHIAGTATAVYFCLGGLLLGGIGTFIIALLPSDTTWPIIAYCLILAIAVLCLSCFNPNRHHPSDDEHDSLATQDIGRSQSGHGHD"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmlB1", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39133", "model_name": "cmlB1", "model_type_id": "40292"}, "328": {"model_id": "328", "ARO_accession": "3002691", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlA is a plasmid-encoded chloramphenicol exporter that is found in Salmonella typhimurium", "model_sequences": {"sequence": {"623": {"dna_sequence": {"fmax": "2858", "fmin": "1685", "accession": "AJ487033", "strand": "+", "sequence": "ATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCAAACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTTGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGGAAGTACATCAAATCCCAATCGTTGAG"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Salmonella enterica subsp. enterica serovar Typhimurium", "NCBI_taxonomy_id": "90371", "NCBI_taxonomy_cvterm_id": "35732"}, "protein_sequence": {"accession": "CAD31707.1", "sequence": "MDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLANVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWALQSVLGFIAPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAGSTSNPNR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmlA", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39125", "model_name": "cmlA", "model_type_id": "40292"}, "1037": {"model_id": "1037", "ARO_accession": "3002693", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlA1 is a plasmid or transposon-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa and Klebsiella pneumoniae", "model_sequences": {"sequence": {"617": {"dna_sequence": {"fmax": "2764", "fmin": "1504", "accession": "AF458080", "strand": "+", "sequence": "GTGCGCTCAAAAAATTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCGGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACGTTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACAGCTCGTTTTATGGGGCGTGTAATACCCAAGTGGGGCAGCCCAAGCGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTTCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGCGGAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACGTCAAATCCCAATCGTTGAG"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "AAO15535.1", "sequence": "MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFISPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRAEGSRGQGEHDVVALQSAESTSNPNR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmlA1", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39127", "model_name": "cmlA1", "model_type_id": "40292"}, "2769": {"model_id": "2769", "ARO_accession": "3004101", "ARO_name": "MdtNOP", "ARO_description": "MdtNOP is a MFS efflux pump protein found in E. coli. The deletion of mdtP from strain W3110 resulted in increased susceptibility to acriflavin, puromycin, and tetraphenylarsonium chloride. An E. coli mdtN null mutant is more sensitive to sulfur drugs than wild type", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"blastp_bit_score": {"param_value": "1442,2056,45,2330", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "41212", "model_name": "MdtNOP", "model_type_id": "41112"}, "2768": {"model_id": "2768", "ARO_accession": "3000788", "ARO_name": "MdtEF-TolC", "ARO_description": "MdtEF-TolC is a multidrug efflux complex in Gram-negative bacteria, including E. coli. MdtE is the membrane fusion protein, MdtF is the inner membrane transporter, while TolC is the outer membrane channel.", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"41141": {"param_value": {"7750": "1903,121,826,869,1015,1318,91,1248,2324"}, "param_type_id": "41141", "param_type": "efflux pump components", "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "37168", "model_name": "MdtEF-TolC", "model_type_id": "41112"}, "2763": {"model_id": "2763", "ARO_accession": "3000787", "ARO_name": "MdtABC-TolC", "ARO_description": "MdtABC-TolC is a multidrug efflux system in Gram-negative bacteria, including E. coli and Salmonella. MdtA is a membrane fusion protein; TolC is the outer membrane channel; MdtBC form a drug transporter. In the absence of MdtB, the MdtAC-TolC has narrower drug specificity, leading to the loss of novobiocin resistance, for example.", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"41141": {"param_value": {"7745": "387,820,1315,826,986,1337,152,2764"}, "param_type_id": "41141", "param_type": "efflux pump components", "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "37167", "model_name": "MdtABC-TolC", "model_type_id": "41112"}, "2762": {"model_id": "2762", "ARO_accession": "3003703", "ARO_name": "MexMN-OprM", "ARO_description": "MexMN-OprM is a multidrug efflux pump expressed in Pseudomonas aeruginosa. MexM is the membrane fusion protein; MexN is the inner membrane transporter; and OprM is the outer membrane channel.", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"41141": {"param_value": {"7744": "2216,2217,1305"}, "param_type_id": "41141", "param_type": "efflux pump components", "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "40357", "model_name": "MexMN-OprM", "model_type_id": "41112"}, "2761": {"model_id": "2761", "ARO_accession": "3003697", "ARO_name": "MexPQ-OpmE", "ARO_description": "MexPQ-OpmE multidrug efflux pump expressed in Pseudomonas aeruginosa. MexP is the membrane fusion protein; MexQ is the inner membrane transporter; and OpmE is the outer membrane channel.", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"41141": {"param_value": {"7743": "2211,2212,2213"}, "param_type_id": "41141", "param_type": "efflux pump components", "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "40349", "model_name": "MexPQ-OpmE", "model_type_id": "41112"}, "2760": {"model_id": "2760", "ARO_accession": "3000799", "ARO_name": "MexGHI-OpmD", "ARO_description": "MexGHI-OpmD is an efflux complex expressed in Pseudomonas aeruginosa. MexG is a membrane protein required for drug export; MexH is the membrane fusion protein; MexI is the inner membrane transporter; and MexJ is the outer membrane channel protein. MexGHI-OpmD confers resistance to vanadium, norfloxacin, and acriflavin.", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"41141": {"param_value": {"7742": "995,1344,1647,442"}, "param_type_id": "41141", "param_type": "efflux pump components", "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "37179", "model_name": "MexGHI-OpmD", "model_type_id": "41112"}, "2766": {"model_id": "2766", "ARO_accession": "3000373", "ARO_name": "EmrKY-TolC", "ARO_description": "EmrKY is a homolog of EmrAB found in E. coli. Together with TolC, it is a tripartite multidrug transporter.", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"41141": {"param_value": {"7748": "609,540,826,1318,1015,1248"}, "param_type_id": "41141", "param_type": "efflux pump components", "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "36512", "model_name": "EmrKY-TolC", "model_type_id": "41112"}, "2765": {"model_id": "2765", "ARO_accession": "3000344", "ARO_name": "EmrAB-TolC", "ARO_description": "EmrAB-TolC is a multidrug efflux system found in E. coli. EmrB is the electrochemical-gradient powered transporter; EmrA is the linker; and TolC is the outer membrane channel. It confers resistance to nalidixic acid and thiolactomycin.", "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "model_param": {"41141": {"param_value": {"7747": "1757,1847,826,1330"}, "param_type_id": "41141", "param_type": "efflux pump components", "param_description": "This parameter describes efflux pump components that are to be detected together (e.g., efflux pump subunits and regulators) using sequential model IDs, separated by commas. For example: 2685,440,1925,1305."}}, "model_type": "efflux pump system meta-model", "model_description": "A meta-model used to detect an efflux pump (and its subunits) along with its regulators and any determinants of overexpression (e.g., mutations in efflux pump subunits, mutations in local and global regulators, mutations in two component regulatory systems)", "ARO_id": "36483", "model_name": "EmrAB-TolC", "model_type_id": "41112"}, "2764": {"model_id": "2764", "ARO_accession": "3004055", "model_param": {"blastp_bit_score": {"param_value": "400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "The Escherichia coli CpxR/CpxA system responds to general periplasmic stress and has been used as a model two-component system for transcription regulation in bacteria. CpxR/CpxA system facilitates Salmonella and E. coli resistance to cationic antimicrobial peptides.The CpxR/CpxA system can activate transcription of marRAB operon, thus facilitating multidrug-resistant regulator to enhance expression of TolC-dependent tripartite multidrug transporters.", "model_sequences": {"sequence": {"4081": {"dna_sequence": {"fmax": "3010538", "fmin": "3009839", "accession": "CP015085.1", "strand": "-", "sequence": "TCATGAAGCAGAAACCATCAGATAGCCGCGACCACGCAAGGTTTTAAACCACGGGTGACCATCTTTACGATCCGGCAGTTTACGACGCAGGTTGGAAATGTGCATATCGATAGCGCGGTCGAAAGGCGTCAGGCGCTTGCCCAGCACTTCCTGGCTTAAATGCTCACGGGAAACCACCTGACCCAGATGCTGTGCCAGCAAATAGAGCAGGGTAAACTCCGTACCGGTTAACTCCAGCGTTTGCCCGTCGAAGGTGGCTTCCTGGCGACCAGGATTGAGACTTAAGGCATCAACTTCCAGTGTCGGTGAACCGTTGTCGTTGTTTTGCTGTTGTTCGCTCCAGTGCGAACGGCGCAGGATCGCGCGAATACGTGCCACCAGCTCACGATCATTAAACGGTTTCGGGAGATAGTCATCTGCGCCCAGCTCAAGGCCGAGAACGCGATCAAGTTCACTGCCGCGCGCCGTCAACATAATGACAGGCGTCTGGTGTGTCTGGCGAAGTGCTTTTAATGTGTCGATACCATTTTTCTTCGGCATCATTACATCAAGCAAAAGTAAATCAATGCTGTCGTCCAGAAGATCAAGCGCCTGTTCCCCATCGTGGGCAACAATCACGTTGAAGCCTTCCATCTCGAGCAGCTCCTTTAATAGGGAAGTCAGCTCTCGGTCATCATCAACTAACAGGATTTTATTCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli O25b:H4", "NCBI_taxonomy_id": "941280", "NCBI_taxonomy_cvterm_id": "40530"}, "protein_sequence": {"accession": "ANK04473.1", "sequence": "MNKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLDDSIDLLLLDVMMPKKNGIDTLKALRQTHQTPVIMLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSHWSEQQQNNDNGSPTLEVDALSLNPGRQEATFDGQTLELTGTEFTLLYLLAQHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDRKDGHPWFKTLRGRGYLMVSAS"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}, "ARO_name": "Escherichia coli CpxR", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41120", "model_name": "Escherichia coli CpxR", "model_type_id": "40292"}, "245": {"model_id": "245", "ARO_accession": "3002695", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlA5 is a plasmid or transposon-encoded chloramphenicol exporter that is found in Escherichia coli", "model_sequences": {"sequence": {"695": {"dna_sequence": {"fmax": "4597", "fmin": "3337", "accession": "AY115475", "strand": "+", "sequence": "GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGTCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACATCAAATCCCAATCGTTGAG"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "AAM77075.1", "sequence": "MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFIAPMWLVGIGVATAVSVSPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAESTSNPNR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmlA5", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39129", "model_name": "cmlA5", "model_type_id": "40292"}, "2792": {"model_id": "2792", "ARO_accession": "3004138", "model_param": {"blastn_bit_score": {"param_value": "5000", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}, "snp": {"param_type": "single resistance variant", "param_value": {"7794": "A2330T"}, "clinical": {"7794": "A2330T"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Point mutations in the 23S ribosomal RNA subunit of M. catarrhalis shown clinically to confer resistance to macrolide class antibiotics.", "model_sequences": {"sequence": {"4107": {"dna_sequence": {"fmax": "3156", "fmin": "0", "accession": "NG_041971.1", "strand": "+", "sequence": "TCAAGTAATGAAGTGCACATGGTGGATGCCTTGGCAGTCAGAGGCGATGAAAGACGTGATAGCCTGCGATAAGCGTCGGTGAGGTGGCAATATCCTGTGACCCGGCGATTTCTGAATGGGGAAACCCAACCAACATAAGTTGGTTATTACACAGTTTACTGTGTAAGGCAAACCGGGAGAAGTGAAACATCTCAGTACCCCGAGGAAAAGACATCAAATGAGATTCCGTAAGTAGCGGCGAGCGAACACGGAGGAGCCGATCAATTTTACAGTAGCAAAATGGCGTGGGAAAGCCAACCATAGTAGGTGATAGTCCTGTATGCGAAACTGTTTAAGCGACATATTAAGTAGGGCGGAACACGAGAAATTCTGTCTGAAGATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCTGTTAGGGGAGTGAAATAGAACCTGAAACCGTGTGCATACAAGCAGTCGGAGCCCGACCACTTAATCGTTTTGAGGATAACAATGAATTTTTACTACGTCTATGTCATACAAAACGTGGATAATCATGATGAGTTTTATGTTGGTTTTACCACCAGTTTAAAACAAAGAATTGATGACCATAATAATGGCACAACTTACTCAACCAGAGCAAGAACATGGCGTATTGTTTATTGTGAAGCCTACATTAATGAACAAGTGGCAAGAAAACGAGAGCGAACCATAAAAAATAATGGTCGTATGAGAACTTTCTTGATGAATCGTGTCAAATCACAATTTGACAATCAGAACGATTAAGTGGTCGGGTGACGGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGTAGGGAAACCGAGTCTTAATAGGGCGAATGAGTTGCAGGGTATAGACCCGAAACCGAGTGATCTATCCATGAGCAGGTTGAAAGTGCCGTAACAGGCACCGGAGGACCGAACCCACTGTCGTTGAAAAGCCAGGGGATGACTTGTGGATAGGGGTGAAAGGCTAATCAAACTCGGTGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGGACGAATACCATTGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCACACCGACTTACCAAACCGATGCAAACTCCGAATACCGATGAGTAATATCCGGGAGACAGACGGCGGGTGCTAACGTCCGTCGTCAAGAGGGAAACAACCCAGACCGCCAGCTAAGGCCCCAAATTCCTAGTTAAGTGGGAAACGATGTGGGAAGGCACAGACAGCTAGGAGGTTGGCTTAGAAGCAGCCACCCTTTAAAGAAAGCGTAATAGCTCACTAGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTCAAACTAGGAGCCGAAGCTGCGGATTTAATTGTTTCAATTAAGTGGTAGGGGAGCGTTGTGTAAGCCTGTGAAGGTGCACTGTAAGGTGTGCTGGAGGTATCACAAGAGCGAATGCTGACGTGAGTAACGACAAAACGGGTGAAAAGCCCGTTCGCCGGAAGACCAAGGGTTCCAGTCCAACGTTAATCGGGGCTGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAATCGGTTAATATTCCGATACTTGTTTATGATGCGATGGAGGGACGGAGAAGGTTATGCCAGCCTGGCGATGGTTGTCCAGGTGGAAGGATGTAGTTAGACTGAGTAGGCAAATCCGCTCGGTTATTAATGAGATCTGATAGCAAGCCAGTTTACTGGCAAAGTGGCAAATACCCTGCTTCCAGGAAAAGCTTCTAAGCGATAGTCATAAACGAATCGTACCCGAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCTGCTGAAGGAACTAGGCAAAATGGTACCGTAACTTCGGGAGAAGGTACGCTGCCGATGGTGATAAGACTTGCTCTTTGAGCTGTTGGCAGTCGCAGATACCAGGCTGCTGCAACTGTTTATTAAAAACACAGCACTCTGCAAACACGAAAGTGGACGTATAGGGTGTGATGCCTGCCCGGTGCTGGAAGGTTAATTGATGGGGTTAGCGTAAGCGAAGCTCTTGATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCATAATGATGGCAGCGCTGTCTCCAGCAGAGACTCAGTGAAATCGAAATCGCAGTGAAGATGCTGTGTACCCGCGGCTAGACGGAAAGACCCCGTGAACCTTTACTACAGCTTTACATTGAACTTTGACCTAACTTGTGTAGGATAGGTGGGAGGCTTTGAAGCAGATACGCCAGTATTTGTGGAGCCAACCTTGAAATACCACCCTGGTTATGTTGGGGTTCTAACTTAGGATCAACAAATCCAAGGACAATGTATGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGTACGAAGGTGCGCTCAGAACGGTCGGAAATCGTTCAAAGAGTATAAAGGCAAAAGCGCGCTTAACTGCGAGACCCACAAGTCGAGCAGGTACGAAAGTAGGTCTTAGTGATCCGGTGGTTCTGTATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCTGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGAAGCAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGAGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTACCGTGGGCGTTGGAAATTTGAGAGGATCTGCTCCTAGTACGAGAGGACCAGAGTGGACGAACCTCTGGTGTTTCGGTTGTCACGCCAGTGGCATTGCCGAGTAGCTATGTTCGGATGGGATAACCGCTGAAAGCATCTAAGCGGGAAGCCCACCTCAAGATAAGATTTCCCTAAAGAGCCGTTGTAGACGACGACGTTGATAGGTTGGGTGTGGAAGTGTAGTGATACATGTAGCTAACCAATACTAATTGCTCGTTTGGCTTGACCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella catarrhalis", "NCBI_taxonomy_id": "480", "NCBI_taxonomy_cvterm_id": "41250"}, "protein_sequence": {"accession": "", "sequence": ""}}}}, "ARO_category": {"35950": {"category_aro_name": "antibiotic resistant gene variant or mutant", "category_aro_cvterm_id": "35950", "category_aro_accession": "0000031", "category_aro_description": "Resistance to antibiotics is often conferred by single nucleotide polymorphisms (SNPs) and other mutations in target genes."}}, "ARO_name": "Moraxella catarrhalis 23S rRNA with mutation conferring resistance to macrolide antibiotics", "model_type": "rRNA mutation model", "model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "ARO_id": "41265", "model_name": "Moraxella catarrhalis 23S rRNA with mutation conferring resistance to macrolide antibiotics", "model_type_id": "40295"}, "486": {"model_id": "486", "ARO_accession": "3002698", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlB is a plasmid-encoded chloramphenicol exporter that is found in Enterobacter aerogenes", "model_sequences": {"sequence": {"17": {"dna_sequence": {"fmax": "1230", "fmin": "0", "accession": "AF034958", "strand": "+", "sequence": "GTGCGCTCAAAGAACTGTAATTGGCGGTATTCCCTTGCCGTCACTGTGTTGTTGTTATCACCTTTCGATTTACTGGCATCACTCGGCATGGACATGTACTTGCCAGCGGTGCCTTTCATGCCACATGCTCTTGGTACGACAGCGGGCACAATTCAGCTTACGCTGACAACGTATTTGGTCATGATAGGGGCCGGTCAGCTTTTGTTTGGGCCACTGTCGGACCGGCTGGGACGTCGTCCCGTGCTACTGGCGGGCGGTGCCGCCTACGTTGCGGCCTCAATCGGCCTCGTCGTCACGTCATCGGCTGGAGTATTTCTGGGTTTTCGGATTCTCCAAGCTTGTGGTGCCTCGGCATGCCTTGTTGCCACATTTGCAACAGTGCGTGATATCTACGCAGGTCGCAAGGAAAGTAACGTCATCTACGGCTTGCTTGGCTCTATGCTTGCTATGGTTCCGGCGATAGGCCCATTGCTGGGAGCGGTCATAGACACCTGGTTCGGGTGGCGGGCGATCTTTGCGTTCTTGGGATTGGGAATGATCGCTGCATTGACAGCAGCGTGGCGGCTCTGGCCTGAGACCCGGGTGCAGCGACCAGCAGCTTTGCAATGGTCACAACTTCTGCTTCCCATCAAGCACCTTAACTTCTGGTTGTACACAGTGTGTTATGCCGCAGGAATGGGCAGCTTCTTCGTCTTCTTCTCCATAGCGCCCGGATTGATGATGGGTAGGCAAGGCATGTCCCAGTTTGGCTTCAGTCTGTTGTTCGCAACAGTGGCAATTGCGATGATGCTTGCGGCCCGCTTCATGGGGCGCGTAATCGCCAAGTGGGGCAGCCTGAGTGCCTTGCGAATGGGGATGGGCTGCCTGATAGCAGGCGCAGTCTTGCTTGTCATCACCGAGCTATGGATTCCGCAGTCCGTGTTGGGCTTTATTGCCCCAATGTGGCTAGTGGGCGTCGGCGTCGCGACAGCGGTATCCGTTGCACCCAATGGTGCGCTTCGAGGGTTCGACCATATTGCAGGAGCCGTTACGGCAGTCTACTTCTGCTTGGGGGGGCTGCTGCTGGGGAGTGTTGGAACGCTCATCATTTCGCTGTTGCCGCGCGACACGGCCTGGCCAGTTATCGCGTATTGTTTGGTTCTTGCAACAATCGTGCTTGGACTGTCGTGTGTTTCCCGAGCGAGAGACCTTCGCGGTCACGGGGAGTATGATGCGGTTGCACGCACATAG"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter aerogenes", "NCBI_taxonomy_id": "548", "NCBI_taxonomy_cvterm_id": "36770"}, "protein_sequence": {"accession": "AAD22144.1", "sequence": "MRSKNCNWRYSLAVTVLLLSPFDLLASLGMDMYLPAVPFMPHALGTTAGTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLAGGAAYVAASIGLVVTSSAGVFLGFRILQACGASACLVATFATVRDIYAGRKESNVIYGLLGSMLAMVPAIGPLLGAVIDTWFGWRAIFAFLGLGMIAALTAAWRLWPETRVQRPAALQWSQLLLPIKHLNFWLYTVCYAAGMGSFFVFFSIAPGLMMGRQGMSQFGFSLLFATVAIAMMLAARFMGRVIAKWGSLSALRMGMGCLIAGAVLLVITELWIPQSVLGFIAPMWLVGVGVATAVSVAPNGALRGFDHIAGAVTAVYFCLGGLLLGSVGTLIISLLPRDTAWPVIAYCLVLATIVLGLSCVSRARDLRGHGEYDAVART"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmlB", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39132", "model_name": "cmlB", "model_type_id": "40292"}, "1435": {"model_id": "1435", "ARO_accession": "3002696", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmlA6 is a plasmid-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa", "model_sequences": {"sequence": {"728": {"dna_sequence": {"fmax": "4009", "fmin": "2749", "accession": "AF294653", "strand": "+", "sequence": "GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATAGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTTGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACATCAAATCCCAATCGTTGAG"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AAK52606.1", "sequence": "MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAIVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWALQSVLGFIAPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAESTSNPNR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmlA6", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39130", "model_name": "cmlA6", "model_type_id": "40292"}, "907": {"model_id": "907", "ARO_accession": "3002704", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "fexA is a plasmid-encoded chloramphenicol exporter that is found in Staphylococcus lentus", "model_sequences": {"sequence": {"490": {"dna_sequence": {"fmax": "1604", "fmin": "176", "accession": "AJ549214", "strand": "+", "sequence": "ATGAAAAAGGATAGTAAATCTAAAGAAATGATTCAATCTGAAAAAAGGGGTTCTACTAGGCTTTTAATGATGGTACTCTCCCTATCTGTACTTGTAGGTGCAATTACGGCTGATTTAGTCAATCCCGTACTTCCACTAATAAGCAAAGATTTAGAAGCTTCGAAATCTCAAGTGAGTTGGATAGTTAGTGGTATTGCACTTGTTCTTGCGATTGGAGTTCCGATTTATGGTCGAATCTCAGACTTTTTTGAGTTACGAAAGCTATATATCTTTGCCATTATGATTCTGGCAAGTGGTAGTCTTTTATGTGCAATTGCCCCGAACCTCCCATTGTTGGTTTTGGGAAGAATGGTTCAGGGTGCTGGGATGTCCGCAATTCCAGTTCTATCAATCATTGCAATTTCGAAGGTTTTCCCACAAGGAAAACGTGGGGGAGCTTTGGGAATTATCGCAGGAAGTATTGGTGTTGGAACTGCTGCTGGTCCAATATTTGGTGGAGTAGTTGGTCAATATTTAGGGTGGAATGCCTTGTTTTGGTTCACATTTTTGTTAGCCATTATGATTGTTATTGGTGCCTACTACGCGTTACCGACAATTAAACCGGCAGAATCCGTAGGAAGCAATAAGAACTTTGATTTCATTGGTGGTTTATTCCTCGGCCTCACAGTAGGATTACTCCTTTTTGGCATCACTCAAGGAGAAACTTCTGGTTTTTCTTCGTTCTCATCGTTAACTAGCCTAATTGGTTCTGTTGTAGCTTTGGTGGGATTTATTTGGAGAATTGTTACCGCAGAAAATCCATTTGTACCACCTGTCCTGTTCAATAACAAGGATTATGTCAATACGGTCATAATTGCATTTTTTTCGATGTTTGCTTATTTCGCTGTTCTTGTGTTCGTCCCATTACTAGTCGTTGAGGTGAATGGACTCTCTTCTGGACAGGCTGGAATGATATTGTTGCCAGGTGGTGTGGCTGTTGCAATCTTATCTCCCTTCGTTGGCCGTCTTTCTGATCGATTTGGGGATAAACGTCTGATAATTACTGGGATGACTCTGATGGGGCTGTCTACCTTATTCTTGTCCACCTATGCATCTGGTGCTTCACCTCTGTTAGTTTCCGTGGGGGTCCTCGGAGTAGGGATTGCTTTTGCATTCACGAATTCTCCCGCAAATAACGCCGCAGTAAGTGCACTCGATGCAGACAAGGTTGGTGTCGGAATGGGGATTTTCCAAGGTGCTTTGTACCTTGGAGCAGGAACTGGAGCAGGTATGATTGGAGCATTATTATCCGCTCGACGTGATGCTACTGAGCCGATAAATCCATTATATATATTGGACGCTATGTCCTACTCAGATGCGTTCCTTGCAGCTACAGGGGCAATACTCATTGCCTTAATAGCTGGATTAGGTTTAAAAAAGCGTGGGTAAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus lentus", "NCBI_taxonomy_id": "42858", "NCBI_taxonomy_cvterm_id": "39555"}, "protein_sequence": {"accession": "CAD70268.1", "sequence": "MKKDSKSKEMIQSEKRGSTRLLMMVLSLSVLVGAITADLVNPVLPLISKDLEASKSQVSWIVSGIALVLAIGVPIYGRISDFFELRKLYIFAIMILASGSLLCAIAPNLPLLVLGRMVQGAGMSAIPVLSIIAISKVFPQGKRGGALGIIAGSIGVGTAAGPIFGGVVGQYLGWNALFWFTFLLAIMIVIGAYYALPTIKPAESVGSNKNFDFIGGLFLGLTVGLLLFGITQGETSGFSSFSSLTSLIGSVVALVGFIWRIVTAENPFVPPVLFNNKDYVNTVIIAFFSMFAYFAVLVFVPLLVVEVNGLSSGQAGMILLPGGVAVAILSPFVGRLSDRFGDKRLIITGMTLMGLSTLFLSTYASGASPLLVSVGVLGVGIAFAFTNSPANNAAVSALDADKVGVGMGIFQGALYLGAGTGAGMIGALLSARRDATEPINPLYILDAMSYSDAFLAATGAILIALIAGLGLKKRG"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "fexA", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39138", "model_name": "fexA", "model_type_id": "40292"}, "2783": {"model_id": "2783", "ARO_accession": "3004118", "ARO_description": "A ToxR negatively regulated outer membrane porin. In Vibrio cholerae, ToxR controls resistance to P2 (a BPI-derived antimicrobial peptide) by regulating the production of OmpT, especially in the absence of OmpU.", "model_sequences": {"sequence": {"4105": {"dna_sequence": {"fmax": "1821", "fmin": "786", "accession": "AF079766", "strand": "+", "sequence": "ATGAAAAAAACTCTATTAGCACTCGCAGTGCTTGCAGCCGCAGGCTCTGTAAACGCAGCTGAAATTCTAAAATCAGATGCTGGCACTGTTGATTTTTACGGTCAGCTACGTACAGAATTGAAATTCTTAGAAGATAAAGATCCAACAATTGGTTCTGGTTCTTCGCGCGCTGGTGTTGATGCAAACTACACCGTTAACGATAGCTTAGCGTTACAAGGTAAAGTGGAATTCGCACTAAAAGACAGTGGCGATATGTATGTTCGTAACCACATTCTTGGTGTAAAAACTAATTTTGGTAAGTTTAGCTTTGGTAAACAATGGACTACATCTGACGATGTATACGGTGCTGACTACTCTTATTTCTTTGGTGGTACAGGTCTTCGTTACGGCACACTGTCTGATGCACTACACGATTCTCAAGTCAAGTATGTTTACGAAGCTGACAGCTTCTGGGTTAAAGCTGGTTACGGTTTTCCAGAAGATAATGCAAAGCAAGAGCTAGCAGAACTGTATGTAGGTGCAACATTTGGTGATTTGGCTGTGCACGCTGGTGGTGGTCAAAACCGTGATAAAGCATTCAAAGTTGGTAGTAATACGGTTGGCACAACAACCACAGATATTAAAGCTGACGTAACAAATAGTTACTTTGAAGTGACAGGTGAGTACACTATTGGTGATGCACTGATTGGTGTTACTTACTACAACGCAGAACTAGATGTAGAAAATAACCCACTAGTGATCGATGAAGACGCTATTTCTGTTGCTGGTACATACAAAGTTGCTGACAAGACAAAATTGTATGCTGGCTATGAGTATGTAATGCAAGAAGCGAACACTGGCGCAGATGAAGATGGTACTCTTGTTTACCTAGGTGTTGAATACAAATTTGCAAGCTGGGCTCGTGTATATGCTGAGTATGGCTACGGCGATGGTACAACTCTGGGTTACACCAACAAGGGTTCTGACGCAGAAGTTAAAGCAACGAAAGTCGACAGCGCTAATAACTTTGGTATCGGCGCTCGTATCTACTGGTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio cholerae", "NCBI_taxonomy_id": "666", "NCBI_taxonomy_cvterm_id": "36789"}, "protein_sequence": {"accession": "AAC28105", "sequence": "MKKTLLALAVLAAAGSVNAAEILKSDAGTVDFYGQLRTELKFLEDKDPTIGSGSSRAGVDANYTVNDSLALQGKVEFALKDSGDMYVRNHILGVKTNFGKFSFGKQWTTSDDVYGADYSYFFGGTGLRYGTLSDALHDSQVKYVYEADSFWVKAGYGFPEDNAKQELAELYVGATFGDLAVHAGGGQNRDKAFKVGSNTVGTTTTDIKADVTNSYFEVTGEYTIGDALIGVTYYNAELDVENNPLVIDEDAISVAGTYKVADKTKLYAGYEYVMQEANTGADEDGTLVYLGVEYKFASWARVYAEYGYGDGTTLGYTNKGSDAEVKATKVDSANNFGIGARIYW"}}}}, "ARO_category": {"36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Vibrio cholerae OmpT", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "41242", "model_name": "Vibrio cholerae OmpT", "model_type_id": "40354"}, "1366": {"model_id": "1366", "ARO_accession": "3002703", "model_param": {"blastp_bit_score": {"param_value": "700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmx is a plasmid or transposon-encoded chloramphenicol exporter that is found in Corynebacterium striatum and Pseudomonas aeruginosa.", "model_sequences": {"sequence": {"3": {"dna_sequence": {"fmax": "37110", "fmin": "35934", "accession": "AF024666", "strand": "+", "sequence": "ATGCCTTTTGCCCTCTACATGCTTGCCCTGGCGGTCTTCGTCATGGGCACTTCAGAATTCATGCTCGCGGGATTGCTCCCCGCGATCGCGACCGAACTTGACGTCTCGGTCGGCACTGCGGGCCTGCTGACCTCCGCATTCGCAGTCGGTATGGTCGTCGGCGCGCCAGTGATGGCGGCATTCGCTCGCCGTTGGCCACCGCGGCTCACATTGATCGTTTGCCTTCTCGTGTTCGCGGGAAGCCACGTCATCGGAGCGATGACACCAGTGTTCTCTCTCCTGCTCATCACCCGGGTGCTCAGCGCTCTCGCAAACGCAGGATTCCTCGCCGTAGCACTGAGCACGGCCACTACCCTCGTGCCAGCGAACCAGAAGGGGCGTGCACTGTCGATCCTGCTCTCCGGCACGACGATCGCAACCGTCGTGGGCGTCCCCGCCGGGGCACTGCTCGGCACAGCGCTGGGCTGGCGAACGACGTTCTGGGCGATCGCCATCCTCTGTATTCCCGCGGCCGTTGGAGTCATTCGTGGCGTCACGAACAATGTTGGTCGGAGCGAGACTAGCGCGACCTCACCAAGGCTCCGTGTCGAGCTCAGCCAGTTGGCGACGCCGCGGCTCATCCTGGCCATGGCACTCGGAGCGCTGATCAACGGAGGGACCTTTGCGGCATTCACCTTCCTGGCACCCATCGTGACCGAGACCGCGGGCTTGGCCGAAGCGTGGGTGTCCGTCGCGCTGGTGATGTTCGGCATCGGATCGTTCCTTGGCGTCACGATCGCAGGACGACTATCAGATCAACGACCTGGCCTCGTGCTCGCAGTCGGCGGACCGCTATTGCTGACAGGCTGGATCGTGTTGGCAGTGGTCGCATCTCATCCCGTTGCGCTTATCGTCCTCGTCCTCGTTCAGGGATTCCTGTCGTTCGGCGTCGGCAGTACTCTGATCACGCGTGTGCTGTATGCAGCATCGGGTGCGCCAACGATGGGCGGTTCGTACGCAACCGCAGCATTGAATATCGGAGCTGCAGCGGGGCCCGTGCTTGGTGCGCTCGGGCTCGCGACCGGGCTGGGGCTGCTCGCGCCGGTTTGGGTCGCTTCGGTGCTGACAGCGATCGCTCTCGTCATCATGCTTCTCACCAGACGCGCGCTTACGAAGACCGCGGCGGAGGCCAATTGAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Corynebacterium striatum", "NCBI_taxonomy_id": "43770", "NCBI_taxonomy_cvterm_id": "39554"}, "protein_sequence": {"accession": "AAG03380.1", "sequence": "MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAAFARRWPPRLTLIVCLLVFAGSHVIGAMTPVFSLLLITRVLSALANAGFLAVALSTATTLVPANQKGRALSILLSGTTIATVVGVPAGALLGTALGWRTTFWAIAILCIPAAVGVIRGVTNNVGRSETSATSPRLRVELSQLATPRLILAMALGALINGGTFAAFTFLAPIVTETAGLAEAWVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVLVLVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGALGLATGLGLLAPVWVASVLTAIALVIMLLTRRALTKTAAEAN"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmx", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39137", "model_name": "cmx", "model_type_id": "40292"}, "2798": {"model_id": "2798", "ARO_accession": "3004145", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}, "snp": {"param_type": "single resistance variant", "param_value": {"7819": "V29G"}, "clinical": {"7819": "V29G"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "AxyZ is a transcriptional regulator of the AxyXY-OprZ efflux pump system.", "model_sequences": {"sequence": {"4134": {"dna_sequence": {"fmax": "29177", "fmin": "28538", "accession": "AFRQ01000061.1", "strand": "+", "sequence": "ATGGCCCGCAAGACGAAAGAAGAATCCCAACGCACCCGCGACCGCATCCTGGACGCCGCCGAACACGTGTTCCTGTCCAAGGGCGTGGCCAGCACCACCATGAGCGATATCGCTGATTTCGCGGGCGTGTCCCGGGGCGCCGTCTACGGCCATTACAAGAACAAGATCGATGTCTGCATCGCCATGTGCGACCGGGCCCTGGGGGAAGCGGTGTCGCTGACCCGCGTGTCGACCGACGGCGAGGCGCTGGAAGCGCTCTACGCGTCGATGCGCCAGTACGTGCAGATCTACGCCGAGGAAGGCTCGGTGCAGCGTGTGCTGGAAATCCTCTACCTGAAATGCGAGCGCAGCGACGAGAACGCGCCGCTCCTGCGCCGCCGCGACCTGTGGGAGCGCCACGCCCTGCGCACTTCCGAAAAGTTGCTGCGCGCCGCCGTCAGCCGCGAGGACCTGCCGCCCGCGCTGGACGTGCGTCTGTCCAATGTCTACCTGCACTCCCTGGTCGAGGGCGTGTTTGGCACCATCTGCTGGTCCGATCGCCTCAAGGGCGATATCTGGCCGCGCGTCGAGCGCATGCTCCGCGCCGCCATCGACACGCTGCGCCTGTCGCCGCAACTGCGGTTGCCACAGGCCGCCTGA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter insuavis AXX-A", "NCBI_taxonomy_id": "1003200", "NCBI_taxonomy_cvterm_id": "41271"}, "protein_sequence": {"accession": "EGP45233.1", "sequence": "MARKTKEESQRTRDRILDAAEHVFLSKGVASTTMSDIADFAGVSRGAVYGHYKNKIDVCIAMCDRALGEAVSLTRVSTDGEALEALYASMRQYVQIYAEEGSVQRVLEILYLKCERSDENAPLLRRRDLWERHALRTSEKLLRAAVSREDLPPALDVRLSNVYLHSLVEGVFGTICWSDRLKGDIWPRVERMLRAAIDTLRLSPQLRLPQAA"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}, "35950": {"category_aro_name": "antibiotic resistant gene variant or mutant", "category_aro_cvterm_id": "35950", "category_aro_accession": "0000031", "category_aro_description": "Resistance to antibiotics is often conferred by single nucleotide polymorphisms (SNPs) and other mutations in target genes."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}, "ARO_name": "AxyZ", "model_type": "protein variant model", "model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "ARO_id": "41274", "model_name": "AxyZ", "model_type_id": "40293"}, "2799": {"model_id": "2799", "ARO_accession": "3004144", "model_param": {"blastp_bit_score": {"param_value": "1700", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "AxyY is the periplasmic adaptor protein of the AxyXY-OprZ efflux pump system in Achromobacter spp.", "model_sequences": {"sequence": {"4135": {"dna_sequence": {"fmax": "27124", "fmin": "23986", "accession": "AFRQ01000061.1", "strand": "-", "sequence": "TCATGGCGTCGTCTCCAGCGGTTCGCGGCCGTCGGGGCGCGCGGGGCGGGCGCGCATGCCGACCATGCGTCCCACGATGAGAAAGAACAGCGGCACCAGGAACACCGCCAGCACGGTCGCCGTGATGATCCCGCCCAGCACGCCGGTGCCGATGGCGGCCTGCGCGCCCGAGGCGGCGCCAGTGGCCAGCGCCAGCGGCAGCACGCCCACGCCAAAGGCCAGCGAGGTCATCACGATCGGCCGCAGCCGCAGCCGCGCCGCTTCCAGCGTGGCGGACAGGATGCCCTGGCCGTCGCGCACCAGGTCCTTGGCCACTTCCACGATCAGGATCGCGTTCTTGGCGGACAGGCCGATGGTGGCGATCAGGCCGACCTTGAAGTAGATGTCGTTGGGCATGCCGCGCACGGTCACCCCCAGCAGCGCGCCGATCACGCCCAGCGGCACCACCAGGATCACCGCCAGCGGAATCGACCAGCTTTCATACAGCGCCGCCAGCGCCAGGAACACGATCAGCACCGACAGCGCGAACAGCACCGGCGCCTGGTTGCCGGACAGCCGCTCTTCGTACGATTGGCCCGACCAGTCGAAGCCGATGCCGCGCGGCAGCTCGGCCGCCAGCGTCTCCATGGCGCGCATGGCCTCGCCGCTGCTGTGGCCGCGCGCCGCCGAGCCGTTGATGGTGAACGACGGGAAGCCGTTGTAGCGGTTCAGCTGCGGCGGCCCCATCGACCACGTCAGCGTGGCGAACGCCGACAGCGGCACCATCTGGCCCTGCAGGTTGCGCACGTGCAGGCGCGAGATGTCGTCCACGTCCACGCGGCGCTTGCCGTCGGCCTGCACCATCACGCGCCGAACCTGGCCGTTGAGCATGAAGTCGCCGATGTAGTCCGAGCCGTACATCACAGCCAGCGCGGTGTTGATCTCGTCGATCGGCACGCCCATGGCCTGCGCCTTGTCGCGGTCGACGCGCAGTTGCAGCTGCGGCGCCTCTTCCTGGCCGGCGAACACCACGTCCGTCAGCGCGGGATGCTCGGCCGCCTTGGCCAGCAGCTTCTGGCGCGCCTGCGTCAGGGCTTCGTAGCCGAGGCCGCCGCGATCCTGCAGCCGGAAGTCGAAGCCCGAGGTCGAGCCCAGGTCAGGCAGCGGCGGCGAGTTCAGCGCGAACACCATCAGGTTCTTGCGATCCGCGAACGCCTTGTTGATGCGCTTGACCACCGCGTCCACGTGTTGCGAGGCATCGCGGCGTTCCTTCCAGTCCTTCAGCGTGACGAAGAACATGGCGGAGTTCGGGCCGCTGCCGTACTGGCTGAAGCCGTTGACCGAATACACGTACTGCACCGGCTCGTGCTCCATCATGTAGCGTTCGACGTCCTTGACCACCGCCATGGTCTCGGCCTGCGGCGAGCCCTGCGGCAGGATCACCATGGCCATGAAGCTGCCCTGGTCCTCGTCCGGCAGGAACGACGATGGCAGCCGCGCGAACAGCAACGCCGCCACGCCGATCACCAGCGCATAGGCCAGGCCGAAGCGTACCGGCCGCGCCAGCACGCCGGCCACCCGCGCCGTATAGCGCGTGGTCAGGCGCGCGAAGGCGCGGTTGAACCAGCCGAAGAAGCCGCGCTTCTCGTGGTGGCCGGCCGGGACGGGTTTGAGCAGGCTGGCGCACAGCGCCGGCGTCAGCGACAGCGCCAGGAAGGCCGAGAAGGCGATCGACACCGCCAGCGTCACGGCGAACTGGCGGTAGATGTTGCCCACCGCGCCGTCGAAGAACGCCATCGGCACGAACACCGACACCAGCACCACGGTGATGCCGACGATGGCGCCGCTGATCTGGCCCATGGCCTTGACCGTGGCGTCATGCGGCGACAGGCCTTCCTCGGCCATGATGCGCTCGACGTTCTCGACCACCACGATGGCGTCGTCCACCAGGATGCCGATGGCCAGCACCATGCCGAACATCGTCAGCACGTTGATCGAATAGCCCAGCCCCAGCATCACCCCCAGCGTGCCCAGCAGCGCCACCGGCACCACCAGGGTCGGGATCAGCGTGGCGCGCAGGTTCTGCATGAACAGGTACATCACGCAGAACACCAGCGCCACCGCCTCCAGCAGCGTCATCAGGACCTTCTTGATCGAGATCTCGACGAAGGTGGAGGTCTCGTACGGAATGTCCCAGGTCACGCCCGGCGGGAAGTATTGCGCCAGCTCGCGCATGGTCTCGCGGATGCGGCGGGTGGTTTCGACGGCGTTGGAGCCGGGCGCCAGCTTGATGCCCAGGCCGGTGCCGGTCAGGCCGTTGACGCGCGACAGGTACATGTAGTCGGTGCCGCCCAGCTCCACCCGCGCCACGTCCTTCAGGCGCAGCGTGGCGCCGTCCGGCAGCGCCCGCAGCGGGATGTTGGCGAACTGTTCCGGCGTGTGCAGCGATTCGCCCGCCACGATGCTGGCGTTCAGCGGCGCGTCCTTGGGCACGGCCTGGTTGCCCAGTTCGCCGATGGTGACGCGCGCGTTGTGGCTGCGCAGCGCCGAGACGATGTCGCCCGGCGTCAGCGACAGGGCGGTGAGCTTGGCCGGGTCCGGCCAGATGCGCATCGCCGCTTCCGCGCCGAACGACTGCACCTTGCCCACGCCTTCGACCCGCCGCAGCGCCTGCAGCACATTGGAGGCGGCCAGCTCGCCCAGTTGCATGTCGTCCAGGCTGCCGTCCGACTTCAACGACACCACCAGCTGGATGTTGTCGGCCGCCTTTTCCACGCGCACGCCATCGCGCCGCACCGATTCGGGCAGGCGAGGCTCGACCGCCTTCAGGCGGTTCTGCACTTCCACCGCCGCGATGTCGGGGTTGGTGCCCTGCTTGAAGGTCAGGTTGATGCTGGCCCAGCCGGTCGAATCGCTGCTGGACGAGGTGTACATCAGGCCCGGGGCGCCGTTCATCTCGCGTTCGATGATGGCGGTGACGGCTTCCTCGACCACCTTGGCCGAGGCGCCGGGATAGCTGGCGCCGATGTTGACGACGGGCGGAGCGATGTCCGGATACTGCGCCACCGGCAGCGCGCGGATCGACAACAGGCCGACCAGCGCGATGAGCAGCGAGATCACCCACGCGAAAACGGGGCGATCGATAAAGAAACGCGCCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter insuavis AXX-A", "NCBI_taxonomy_id": "1003200", "NCBI_taxonomy_cvterm_id": "41271"}, "protein_sequence": {"accession": "EGP45231.1", "sequence": "MARFFIDRPVFAWVISLLIALVGLLSIRALPVAQYPDIAPPVVNIGASYPGASAKVVEEAVTAIIEREMNGAPGLMYTSSSSDSTGWASINLTFKQGTNPDIAAVEVQNRLKAVEPRLPESVRRDGVRVEKAADNIQLVVSLKSDGSLDDMQLGELAASNVLQALRRVEGVGKVQSFGAEAAMRIWPDPAKLTALSLTPGDIVSALRSHNARVTIGELGNQAVPKDAPLNASIVAGESLHTPEQFANIPLRALPDGATLRLKDVARVELGGTDYMYLSRVNGLTGTGLGIKLAPGSNAVETTRRIRETMRELAQYFPPGVTWDIPYETSTFVEISIKKVLMTLLEAVALVFCVMYLFMQNLRATLIPTLVVPVALLGTLGVMLGLGYSINVLTMFGMVLAIGILVDDAIVVVENVERIMAEEGLSPHDATVKAMGQISGAIVGITVVLVSVFVPMAFFDGAVGNIYRQFAVTLAVSIAFSAFLALSLTPALCASLLKPVPAGHHEKRGFFGWFNRAFARLTTRYTARVAGVLARPVRFGLAYALVIGVAALLFARLPSSFLPDEDQGSFMAMVILPQGSPQAETMAVVKDVERYMMEHEPVQYVYSVNGFSQYGSGPNSAMFFVTLKDWKERRDASQHVDAVVKRINKAFADRKNLMVFALNSPPLPDLGSTSGFDFRLQDRGGLGYEALTQARQKLLAKAAEHPALTDVVFAGQEEAPQLQLRVDRDKAQAMGVPIDEINTALAVMYGSDYIGDFMLNGQVRRVMVQADGKRRVDVDDISRLHVRNLQGQMVPLSAFATLTWSMGPPQLNRYNGFPSFTINGSAARGHSSGEAMRAMETLAAELPRGIGFDWSGQSYEERLSGNQAPVLFALSVLIVFLALAALYESWSIPLAVILVVPLGVIGALLGVTVRGMPNDIYFKVGLIATIGLSAKNAILIVEVAKDLVRDGQGILSATLEAARLRLRPIVMTSLAFGVGVLPLALATGAASGAQAAIGTGVLGGIITATVLAVFLVPLFFLIVGRMVGMRARPARPDGREPLETTP"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "AxyY", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41273", "model_name": "AxyY", "model_type_id": "40292"}, "2794": {"model_id": "2794", "ARO_accession": "3004134", "model_param": {"blastn_bit_score": {"param_value": "2000", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}, "snp": {"param_type": "single resistance variant", "param_value": {"7799": "A2058G", "7798": "A2058C", "7802": "A2059G", "7801": "A2059C", "7800": "A2058U"}, "clinical": {"7799": "A2058G", "7798": "A2058C", "7802": "A2059G", "7801": "A2059C", "7800": "A2058U"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Point mutations in Helicobacter pylori shown to confer resistance to clarithromycin, a macrolide antibiotic.", "model_sequences": {"sequence": {"4113": {"dna_sequence": {"fmax": "2975", "fmin": "0", "accession": "AB162858.1", "strand": "+", "sequence": "AAGGCAGTGGTAGCGCTGAAGAATATTCGTGCAATTGTCGTTATTCATTATAAAAGGGCAGGTTTTAAAGGATATTTTAAAATTTAAAACAAGCTTTTAAGAGCAGATGGCGGATGCCTTGCCAAAGAGAGGCGATGAAGGACGTACTAGACTGCGATAAGCTATGCGGAGCTGTCAAGGAGCTTTGATGCGTAGATGTCCGAATGGGGCAACCCAACTAATAGAGATATTAGTTACTCTAATTTAGAGAGCGAACCTAGTGAAGTGAAACATCTCAGTAACTAGAGGAAAAGAAATCAACGAGATTCCCTAAGTAGTGGCGAGCGAACGGGGAAAAGGGCAAACCGAGTGCTTGCATTCGGGGTTGAGGACTGCAACATCCAAGAGAACGCTTTAGCAGAGTTACCTGGAAAGGTAAGCCATAGAAAGTGATAGCCTTGTATGCGACAAGGCGTTCTTAGGTAGCAGGATCCAGAGTAGGCCAGGACACGAGAAATCCAGGTTGAAGCTGGGGAGACCACTCTCCAACCCTAAATACTACTCTTTGAGCGATAGCGAACAAGTACCGTGAGGGAAAGGTGAAAAGAACCGCAGTGAGCGGAGTGAAATAGAACCTGAAACCATCTGCTTACAATCATTCAGAGCCCTATGATTTATCAGGGTGATGGACTGCCTTTTGCATAATGATCCTGCGAGTTGTGGTATCTGGCAAGGTTAAGCGGATGCGAAGCCGTAGCGAAAGCGAGTCTTAATAGGGCGGTTTAAGTCAGATGCTGCAGACCCGAAGCTAAGTGATCTATCCATGGCCAAGTTGAAACGCGTGTAATAGCGCGTGGAGGACTGAACTCGTACCCATTGAAACGGGTTGGGATGAGCTGTGGATAGGGGTGAAAGGTCAAACAAACTTAGTGATAGCTGGTTCTCTTCGAAATATATTTAGGTATAGCCTCAAGTGATAATAAAAGGGGGTAGAGCTCTGATTGGGCTAGGGCTGCTCGCCGCGGTACCAAACCCTATCAAACTTCGAATACCTTTTATCGTATCTTGGGAGTCAGGCGGTGGGTGATAAAATCAATCGTCAAAAGGGGAACAACCCAGACTACCAAATAAGGTCCCTAAGTTCTATTCTGAGTGGAAAAAGATGTGTGGCTACTCAAACAACCAGGAGGTTGGCTTAGAAGCAGCCATCCTTTAAAGAAAGCGTAACAGCTCACTGGTCTAGTGGTCATGCGCTGAAAATATAACGGGGCTAAGATAGACACCGAATTTGTAGATTGTGTTAAACACAGTGGTAGAAGAGCGTTCATACCAGCGTTGAAGGTATACCGGTAAGGAGTGCTGGAGCGGTATGAAGTGAGCATGCAGGAATGAGTAACGATAAGATATATGAGAATTGTATCCGCCGTAAATCTAAGGTTTCCTACGCGATGGTCGTCATCGTAGGGTTAGTCGGGTCCTAAGCCGAGTCCGAAAGGGGTAGGTGATGGCAAATTGGTTAATATTCCAATACCGACTCATGGAGCGTGATGGGGGGACGCATAGGGTTAAGCGAGCTAGCTGATGGAAGTGCTAGTCTAAGGGCGTAGATTGGAGGGAAGGCAAATCCACCTCTGTATTTGAAACCCAAACAGGCTCTTTGAGTCCTTTCAGGACAAAGGGAGAATCGCTGATACCGTCGTGCCAAGAAAAGCCTCTAAGCATATCCATAGTCGTCCGTACCGCAAACCGACACAGGTAGATGAGATGAGTATTCTAAGGCGCGTGAAAGAACTCTGGTTAAGGAACTCTGCAAACTAGCACCGTAAGTTCGCGATAAGGTGTGCCGCAGCAATGCGGTCTCAGCAAAGAGTCCCTCCCGACTGTTTACCAAAAACACAGCACTTTGCCAACTCGTAAGAGGAAGTATAAGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAAGAGGATGCGTCAGTCGCAAGATGAAGCGTTGAATTGAAGCCCGAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAGATGGGAGCTGTCTCAACCAGAGATTCAGTGAAATTGTAGTGGAGGTGAAAATTCCTCCTACCCGCGGCAAGACGGAAAGACCCCGTGGACCTTTACTACAACTTAGCACTGCTAACGGGAATATCATGTGCAGGATAGGTGGGAGGCTTTGAAGTAAGGGCTTTGGCTCTTATGGAGCCATCCTTGAGATACCACCCTTGATGTTTCTGTTAGCTAACTGGCCTGTGTTATCCACAGGCAGGACAATGCTTGGTGGGTAGTTTGACTGGGGCGGTCGCCTCCTAAAAAGTAACGGAGGCTTGCAAAGGTTGGCTCATTGCGGTTGGAAATCGCAAGTTGAGTGTAATGGCACAAGCCAGCCTGACTGTAAGACATACAAGTCAAGCAGAGACGAAAGTCGGTCATAGTGATCCGGTGGTTCTGTGTGGAAGGGCCATCGCTCAAAGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAGGAAAGTTGAGGAGAGCTGTCCCTAGTACGAGAGGACCGGGATGGACGTGTCACTGGTGCACCAGTTGTTCTGCCAAGAGCATCGCTGGGTAGCTACACACGGATGTGATAACTGCTGAAAGCATCTAAGCAGGAAGCCAACTCCAAGATAAACTTTCCCTGAAGCTCGCACAAAGACTATGTGCTTGATAGGGTAGATGTGTAAGCGCAGTAATGCGTTTAGCTGACTACTACTAATAGAGCGTTTGGCTTGTTTTT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Helicobacter pylori", "NCBI_taxonomy_id": "210", "NCBI_taxonomy_cvterm_id": "36906"}, "protein_sequence": {"accession": "", "sequence": ""}}}}, "ARO_category": {"35950": {"category_aro_name": "antibiotic resistant gene variant or mutant", "category_aro_cvterm_id": "35950", "category_aro_accession": "0000031", "category_aro_description": "Resistance to antibiotics is often conferred by single nucleotide polymorphisms (SNPs) and other mutations in target genes."}}, "ARO_name": "Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin", "model_type": "rRNA mutation model", "model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "ARO_id": "41261", "model_name": "Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin", "model_type_id": "40295"}, "1744": {"model_id": "1744", "ARO_accession": "3002702", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "cmrA is a transposon-encoded chloramphenicol exporter that is found in Rhodococcus rhodochrous", "model_sequences": {"sequence": {"699": {"dna_sequence": {"fmax": "1611", "fmin": "435", "accession": "AF015087", "strand": "+", "sequence": "GTGCCTTTCGCTATCTACGTCCTCGGGCTTGCCGTCTTTGCCCAGGGCACATCCGAATTCATGTTGTCCGGGCTCATACCGGATATGGCCCGCGACCTCGGCGTCTCGGTCCCCGCCGCCGGACTCCTCACCTCCGCCTTCGCGGTCGGGATGATCATCGGCGCTCCGCTGATGGCCATCGCCAGCATGCGGTGGCCCCGGCGACGCGCCCTTTTGACATTCCTCATCACGTTCATGCTGGTCCACGTCATCGGCGCGCTCACCAGCAGCTTCGAGGTCTTGCTGGTCACACGCATCGTCGGCGCCCTCGCCAACGCCGGATTCTTGGCGGTGGCCCTGGGCGCGGCGATGGCGATGGTGCCCGCCGACATGAAAGGGCGCGCAACGTCCGTCCTCCTCGGTGGTGTCACGATCGCATGTGTAGCCGGAGTTCCCGGGGGCGCCTTCCTCGGTGAAATATGGGGCTGGCGTGCAGCGTTCTGGGCTGTCGTCGTCATCTCCGCCCCTGCGGTGGTGGCGATCATGTTCGCCACCCCGGCCGAGCCGCCAGCAGAGTCCACACCGAACGCCAAGCGTGAACTGTCCTCGCTGCGCTCACGCAAGCTCCAGCTGATGCTTGTCCTCGGTGCCCTGATCAACGGCGCAACATTCTGTTCGTTCACCTACATGGCGCCCACTCTCACCGACATCTCCGGTTTCGACTCCCGTTGGATTCCGTTGCTGCTGGGGTTGTTCGGGCTCGGATCGTTCATCGGCGTCAGCGTCGGAGGCAGGCTCGCCGATACCCGGCCGTTCCAACTTCTCGCCGTGGGATCCGCAGCACTGTTGACGGGATGGATCGTCTTCGCTCTCACGGCATCCCACCCTGCGGTGACATTGGTGATGCTGTTCGTGCAGGGCGCTCTGTCCTTCGCGGTCGGCTCGACCTTGATCTCCCAGGTGCTCTACGCCGCCGACGCGGCGCCGACCTTGGGTGGATCGTTCGCGACGGCCGCGTTCAACGTCGGCGCTGCACTGGGCCCGGCCCTCGGCGGGCTGGCGATCGGTATGGGCCTGAGCTACCGCGCCCCGCTCTGGACGAGCGCCGCGCTGGTGACTCTCGCGATCGTCATCGGCGCAGCCACCTTGTCGCTCTGGCGGCGTCCAGCGTCCGTCCAGGAAACCGTCCCAGCCTGAC"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Rhodococcus rhodochrous", "NCBI_taxonomy_id": "1829", "NCBI_taxonomy_cvterm_id": "39553"}, "protein_sequence": {"accession": "AAC45805.1", "sequence": "MPFAIYVLGLAVFAQGTSEFMLSGLIPDMARDLGVSVPAAGLLTSAFAVGMIIGAPLMAIASMRWPRRRALLTFLITFMLVHVIGALTSSFEVLLVTRIVGALANAGFLAVALGAAMAMVPADMKGRATSVLLGGVTIACVAGVPGGAFLGEIWGWRAAFWAVVVISAPAVVAIMFATPAEPPAESTPNAKRELSSLRSRKLQLMLVLGALINGATFCSFTYMAPTLTDISGFDSRWIPLLLGLFGLGSFIGVSVGGRLADTRPFQLLAVGSAALLTGWIVFALTASHPAVTLVMLFVQGALSFAVGSTLISQVLYAADAAPTLGGSFATAAFNVGAALGPALGGLAIGMGLSYRAPLWTSAALVTLAIVIGAATLSLWRRPASVQETVPA"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "cmrA", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "39136", "model_name": "cmrA", "model_type_id": "40292"}, "2793": {"model_id": "2793", "ARO_accession": "3004132", "model_param": {"blastn_bit_score": {"param_value": "2000", "param_type_id": "41093", "param_type": "BLASTN bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix."}, "snp": {"param_type": "single resistance variant", "param_value": {"7817": "G1628G", "7818": "G1627A"}, "clinical": {"7817": "G1628G", "7818": "G1627A"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Point mutation in 23S rRNA of C. reinhardtii chloroplast shown clinically to confer resistance to Erythromycin, a macrolide antibiotic.", "model_sequences": {"sequence": {"4139": {"dna_sequence": {"fmax": "151993", "fmin": "148590", "accession": "NC_005353.1", "strand": "-", "sequence": "AAGGTCAAAATCAAACGGCCTTTAGTATATCTCGGCTAAAGCCATTGCTGACTGTACACCTGATACCTATATAACGGCTTGTCTAGCCGCGGCCTTAGAGAGCACTCATCTTGAGTTTAGCTTCCTACTTAGATGCTTTCAGCAGTTATCTATCCATGCGTAGCTACCCAGCGTTTCCCATTGGAATGAGAACTGGTACACAATTGGCATGTCCTTTCAGGTCCTCTCGTACTATGAAAGGCTACTCTCAATGCTCTAACGCCTACACCGGATATGGACCAAACTGTCTCACGCATGAAATTTTAAAGCCGAATAAAACTTGCGGTCTTTAAAACTAACCCCTTTACTTTCGTAAAGGCATGGACTATGTCTTCATCCTGCTACTGTTAATGGCAGGAGTCGGCGTATTATACTTTCCCACTCTCGAGAAAATATCCTATAAATCGAGCAACAATAAATAAATTGTATGTAAACATTCTTTTAGAGATTGGCTAAATTTATAAAGTCTCTACGGGGACGATTTCTTTTTTTCACTTAAACTGTCTAGCACAGCACGAACGGTTTCAGAAGTTGTTTTACGCGTCTTCGAATCATTCAGAGCTGCAATTTGATCCACCCATGTACAAACTTCTAAGAATTTGTCCGGGGATTCTTTTGCTGACGGAAGCCGCCAAATAATTTTTAAAACTAAATTTGCTTGTTTTTGTTTTAGTTTTAGAAAAGGTTGTAGTTGTGTTAAAAAATTATGCAAAGGCTTGATTTCGCTTAGAATATAATCCGAAACGCTACCCCTATCTCTTACATAACCAACCCCAATTTCATCCACTAATTTGTCTAAAAACCAACGTCTCTGTGTCTTTTGCGTGACTTGGAACGCGAGTGATAGCTGATGCTTAAATTTATAAGACTGATTAGGCTTAATTTGAGCGATTATGCTACCGTCACCGTCTACAAACCCTGCTAAGTAGAGTAAGAACTCTTTATTATATTTTGTATTCATAAGATGTTTTATTTAATTTATTGAATTATTAAACCAAAAAGAAATGGTCTTCCCTCGGCGTTGCCATCTATTGCCCACGAATGTGGTTTATGCGACAGTTTGTACTTAAAACAATAGGAAGGTTTCACCGATATAAGCCGATACTTTGCTTACATTACTGCAAGCACACGCAGTGTTATTTACGTTTTGAACCCAGCTCACGTACCACTTTAATGGGCGAACAGCCCAACCCTTCGGACCTACTACAGACCGAGGATGTGATGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGAACTCTTGGGGAAGATCAGCCTGTTATCCCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACGCGGCACCGTCGGATCACTAAGGCCGGCTTTCGCCCCTGCTCGACTTGTAGGTCTTGCAGTCAAGCTCCCTTTTGCCTTTACACTCAATGTCTGATTTCCGTCCAGACTGAGGGAACCTTTGCACGCCTCCGTTACCTTTTAGGAGGCATTCGCCCCAAATAAACTGCCCACCTGAAACTGTCAAGGGTCCTGATTCAAGGATCCCCATTAGGATTCTAGCTCTTCCAGAGTGGTCTCTCAATGACGGCTCTAATTACCCCGGAAGGTAATCTTCATAGCCTCCCACCTAGGCTGCGCAAGAAAAGCCCAAACCCAATTCCAAGATACAGTCAAGCTTCATAGGGTCTTTCTGTCCAGGTGTAGGTAGTCCGCATCTTCACGGGACAAGTCTATTTCACCGAGCCTCTCTCCGAGACAGCGCCCAGATCGTTACGCCTTTCGTGCAGGTCGAAACTTACTCGACAATGAATTTCGCTACCTTAGGATCGTTATAGTTACGACCGCCGTTCACCGGGGCTTCGGTCGTCAGCTTTTTTCTTACGAAATAACCAACTTCCTTAACCTTCCGGCACTGGGCAGGCGTCAGCCCCCATATATTGTCTTACGACTTTGCGGAGACCTGTGTTTTTGGTAAACAGTCGCCTGGGCCTGGTCACTGCGACCCACCTTGTTACGGATGGGTGCCCCTTCTTCCGAAGTTACGGGGCCAGTTTGCCGAGTTCCTTAGAGAGAGTTCTCTCGCGCCCCTTGGTATTCTCTACCAACCTACCTGTGTCGGTTTCAGGTACAGGTCATTAAATTATAAAGATGTATGAGCTTTTCTTGGAAGTATGACATCACTAGCTACTCGACGGCGAACCATCAAATAGGGATCACGTCTCCACTCAAGATAGCTTTTTTTCTATCTCTCAACGTCTAAACGCTTCCACTGCAATCCAAAAACAGTTCTAGCTTAGCCTCCTTCGTCCCTCAGATCATAATTTAACTCGTACAGGAATATTAACCTGTTTTCCATCGACGACGCCGTTTGGCCTAGTCTTAGGTCCTGACTAACCCCCCATGGACGAACCTAGTGGAGGAACCCTTAGGTTTTCGGGGCATTGGATTCTCACCAATGTTTTCGTTACTCAAGCCGACATTCTCACTTCCGCTTCGTCCATCCCCACTTACGTGAAAACTTCACCCGAGAGCGGAACGCTCCCCTACCTATAATTTATATAATAAATTATATCACAGCTTCGGCAGGTCACTTAGTCCCGGCCATTATCGGCGCAAGAACGCTTTACCAGTGAGCTATTACGCACTCTTTGAAGGGTGGCTGCTTCTAAGCAAACCTCCTGGTTGTTTCAGCATTCTCACATCCTTTTCCACTTAGTGACCATTTAGGGGCCTTAGCTGGTGATCTGGGCTGTTTCCCTCTTGACAATGAAGCTTATCCCCCACTGTCTCACTGGTTTACGGAAGACATGTCTTGTATTCTGAGTTTGCCACGACTTGGTACCGCTTTCGCAGCCCGCATCGAAACAGTAGCTTTACCCCAAGACAGTTCATCGTTACCGCTGCGCCTCAACGCATTTCGGGGAGATCCAGCTAGCTCCGAGTTCGATTGGAATTTCTCCCCTATTCACAGCTCATCCGCCGATTTTTCAACATCGGTCGGTTCGGACCTCCACTTGGTGTTACCCAAGCTTCATCCTGGCCATGAATAGATCACCCGGGTTCGGGTCCATAAGAAGTGACCATTTGCGCCCTATTCAGACTCGCTTTCGCTTGGGCTCCGGATTTTACTCCTTAACCCAGCCACTCCCTATAAGTCGCCGGCTCATTCTTCAACAGGCACGCGGTCACAAGCATTCTTGCTCCCACTGCTTGTCAGCATACGGTTTCATGTTCTATTTCACTCCCCAACAGGGGTTCTTTTCACCTTTCCCTCGTGGTACTATTTCGCTATCGGTCACTCAGGAGTATTTAGCCTTACGAGGTGGTCCTCGCTGATTCACACGGGATTTCACGTGCCCCATGCTACTCGGGATT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Chlamydomonas reinhardtii", "NCBI_taxonomy_id": "3055", "NCBI_taxonomy_cvterm_id": "40815"}, "protein_sequence": {"accession": "", "sequence": ""}}}}, "ARO_category": {"35950": {"category_aro_name": "antibiotic resistant gene variant or mutant", "category_aro_cvterm_id": "35950", "category_aro_accession": "0000031", "category_aro_description": "Resistance to antibiotics is often conferred by single nucleotide polymorphisms (SNPs) and other mutations in target genes."}}, "ARO_name": "Chlamydomonas reinhardtii 23S rRNA with mutation conferring resistance to Erythromycin", "model_type": "rRNA mutation model", "model_description": "An AMR detection model used to identify ribosomal RNA (rRNA) genes with mutations shown to confer elevated resistance to antibiotic(s) relative to the wild-type rRNA sequence. rRNA mutation models include a reference rRNA sequence, a BLASTN bitscore cutoff and mapped potential resistance variants. A submitted sequence must include a known resistance variant to be detected.", "ARO_id": "41259", "model_name": "Chlamydomonas reinhardtii 23S rRNA with mutation conferring resistance to Erythromycin", "model_type_id": "40295"}, "2790": {"model_id": "2790", "ARO_accession": "3004128", "ARO_description": "Omp1 is an outer membrane porin that confers resistance by absence in S. marcescens.  Resistance to Cefoxitin, Ceftriaxone, Cefotaxime, Moxalactam, Ciprofloxacin, Tetracycline, Chloramphenicol has been demonstrated in clinical isolates.", "model_sequences": {"sequence": {"4104": {"dna_sequence": {"fmax": "4321494", "fmin": "4320303", "accession": "CP005927.1", "strand": "+", "sequence": "ATGTTTGAAAAAATCACCGCCGCACCCGCCGACCCGATCCTGGGCCTGACCGACATTTTCCGCGCCGACGCCCGCCCGAATAAAATCAATTTAGGCATTGGCGTTTATAAAGATGAAACCGGCAAAACCCCGGTGCTGACCAGCGTAAAAAAAGCTGAACAGTATCTGCTGGAAAACGAGACCACCAAAAACTATCTCGGCATTGAAGGCATCCCGGCGTTTGCCAGCTGCACGCAAGAGCTGCTGTTCGGTAAAGAGAGCCCGATCGTCACCGATCGTCGCGCACGCACCGCACAGACGCCAGGCGGCACCGGCGGCTTGCGCGTAGCGGCAGACTTTATCGCCAACCAGACCAGCGCCAAGCGCATCTGGATCAGCAACCCAAGCTGGCCGAACCACAAGAACGTCTTTAGCGCCGTTGGCCTGGAAGTGCTGGAGTACGCCTACTACGACGCAGCCAACCACGCGCTGGATTTTGACGGCCTGCTGAACAGCCTGAAACAGGCTCAGGCCGGTGATGTCGTGTTGTTCCACGGCTGCTGCCATAACCCGACCGGTATCGATCCAACGGCGGAACAGTGGGCGCAGCTGGCTGAGCTTTCCGCCGCCAATGGCTGGCTGCCGCTGTTCGACTTCGCCTACCAGGGCTTCGCCAACGGTCTGGAAGAGGATGCGCAGGGTCTGCGTATTTTCGCCGCCAAACATCAAGAGCTGATCGTCGCCAGCTCCTACTCGAAAAACTTCGGCCTGTACAATGAGCGCGTCGGCGCTTGCACCCTTGTAGCTGCCGATGCCGAAACCGCCGATCGCGCCTTCAGCCAGGTGAAGGCGGCCATTCGTGCCAACTACTCTAACCCGCCGTCGCACGGCGCGGCCGTTGTCGCCACCATTCTGGGCAACGACGCCCTGCGCGCGATGTGGGAGCAGGAGCTGACCGACATGCGCCAGCGCATTCACCGCATGCGTCAGCTGTTCGTGAACACCCTGCAGGAGAAAGGCGCACAACAGGACTTCAGCTTTATCATCCAGCAGAACGGCATGTTCTCATTCAGCGGCCTGACCAAAGAACAGGTGCTGCGTCTGCGTGAAGAGTTCGGCGTATACGCCGTAAACTCGGGCCGGGTGAACGTGGCCGGCATGACGCCGGACAACATGGCACCGCTGTGTGAAGCCATCGTCGCCGTGCTCTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia sp. FS14", "NCBI_taxonomy_id": "1327989", "NCBI_taxonomy_cvterm_id": "41255"}, "protein_sequence": {"accession": "AIA49384.1", "sequence": "MKRNILAVVIPALLAAGAANAAEIYNKDGNKLDLYGKVDGLHYFSDDKGNDGDQTYVRFGFKGETQITDQLTGYGQWEYNVQANHSESQGTEGTKTRLGFAGLKFADYGSFDYGRNYGVLYDVEGWTDMLPEFGGDTYTYTDNFMTGRTNGVATYRNNNFFGLVDGLNFAVQYQGKNQNDGRNVKKQNGDGWGISSTYDIGEGVSFGAAYASSNRTDDQKLRSNERGDKADAWTVGAKYDANNVYLAAMYAETRNMTPFGGGNFGAGCAATDDKCGGFASKTQNFEVTAQYQFDFGLRPEVSYLQSKGKNLNVPGVGSDQDLVKYVSVGTTYYFNKNMSTYVDYKINLLDDNEFTKATGTATDDIVAVGLVYQF"}}}}, "ARO_category": {"40439": {"category_aro_name": "gene conferring resistance via absence", "category_aro_cvterm_id": "40439", "category_aro_accession": "3003768", "category_aro_description": "Deletion of gene or gene product results in resistance. For example, deletion of a porin gene blocks drug from entering the cell."}, "36409": {"category_aro_name": "protein modulating permeability to antibiotic", "category_aro_cvterm_id": "36409", "category_aro_accession": "3000270", "category_aro_description": "Enzymes or other proteins either directly or indirectly reducing overall permeability to antibiotics."}}, "ARO_name": "Serratia marcescens Omp1", "model_type": "protein knockout model", "model_description": "An AMR detection model for instances where the absence of a protein - due to large-scale insertion elements, large deletions, or other methods of protein knockout - confers clinical resistance to a known antibiotic. These models include reference sequences. Protein knockout models are currently in development.", "ARO_id": "41254", "model_name": "Serratia marcescens Omp1", "model_type_id": "40354"}, "2791": {"model_id": "2791", "ARO_accession": "3004097", "model_param": {"blastp_bit_score": {"param_value": "475", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}, "snp": {"param_type": "single resistance variant", "param_value": {"7791": "D222N"}, "clinical": {"7791": "D222N"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "CdsA is a phosphatidate cytidylyltransferase which plays a role in the production of membrane phosphatidylglycerol and cardiolipin.", "model_sequences": {"sequence": {"4106": {"dna_sequence": {"fmax": "220929", "fmin": "220125", "accession": "CP019562.1", "strand": "+", "sequence": "ATGACCAAGGATTTACAAAAGAGAACATTGTTTGCGGTATTGGCCCTGGCGATTTTCCTTCCAGTCTTGTTTGCGGGAGGGCTCTTGTTGCAGATAGGGATTGGCTTGTTAGCGATGCTAGGCGTCCATGAACTCTTGCATATGAAGGGACTAAAGACTATGACCATTGAGGGTGCTTTGACTCTTTTTGCGACCTTCGCTCTCACAGTTCCTTTAGAAAATTACCTAACTTTTTTGCCTGTTGATGGAAATGTGGTTGCCTATAGTGTTCTGATTACCATAATGCTAGGGACGACCGTTTTCAGTAAAAACTATACGATTGAAGATGCCGCTTTTCCAATTGCTGTGAGTTTTTATGTTGGTTTTGGCTTCAATGCCTTACTAGATGCTCGGGTGGCAGGTTTTGACAAGGTACTTTTGGCCCTTTTTATCGTTTGGGCGACAGATAGCGCAGCCTACCTGACAGGGATGAATTTTGGTAAACATAAGTTGGCTCCGAGAGTTTCTCCTAATAAGAGTATTGAGGGCTTTGTCGGTGGTATTCTAGGTGCGGTACTGATAACAGTGATTTTCATGTTAGTGGACAGCACAGTTGCTCTTCCTTATGGGATTTATAGAATGAGTCTCTTTGCTGCCTTCTTCAGTGTGGCCGGTCAGTTTGGTGACTTGATTGAAAGTGCCATGAAACGCCATTTCGGTGTCAAGGATTCTGGCAAATTTATCCCTGGACATGGCGGTGTGTTGGATCGCTTTGACAGCATGCTGATTGTGTTTCCAATGATGCACTTATTTGGCCTGTTTTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Streptococcus oralis", "NCBI_taxonomy_id": "1303", "NCBI_taxonomy_cvterm_id": "39527"}, "protein_sequence": {"accession": "AQA08261.1", "sequence": "MTKDLQKRTLFAVLALAIFLPVLFAGGLLLQIGIGLLAMLGVHELLHMKGLKTMTIEGALTLFATFALTVPLENYLTFLPVDGNVVAYSVLITIMLGTTVFSKNYTIEDAAFPIAVSFYVGFGFNALLDARVAGFDKVLLALFIVWATDSAAYLTGMNFGKHKLAPRVSPNKSIEGFVGGILGAVLITVIFMLVDSTVALPYGIYRMSLFAAFFSVAGQFGDLIESAMKRHFGVKDSGKFIPGHGGVLDRFDSMLIVFPMMHLFGLF"}}}}, "ARO_category": {"37131": {"category_aro_name": "determinant of resistance to peptide antibiotics", "category_aro_cvterm_id": "37131", "category_aro_accession": "3000751", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to peptide antibiotics."}, "35950": {"category_aro_name": "antibiotic resistant gene variant or mutant", "category_aro_cvterm_id": "35950", "category_aro_accession": "0000031", "category_aro_description": "Resistance to antibiotics is often conferred by single nucleotide polymorphisms (SNPs) and other mutations in target genes."}}, "ARO_name": "Streptococcus mitis CdsA with mutation conferring daptomycin resistance", "model_type": "protein variant model", "model_description": "Protein variant models perform a similar search to protein homolog models, but secondarily screen query sequences for curated sets of mutations to differentiate between wild type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. For example, a protein that confers elevated resistance to antibiotic(s) relative to wild type. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations", "ARO_id": "41205", "model_name": "Streptococcus mitis CdsA with mutation conferring daptomycin resistance", "model_type_id": "40293"}, "2796": {"model_id": "2796", "ARO_accession": "3004142", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OprZ is the outer membrane component of the AxyXY-OprZ efflux pump system in Achromobacter spp.", "model_sequences": {"sequence": {"4132": {"dna_sequence": {"fmax": "23990", "fmin": "22598", "accession": "AFRQ01000061.1", "strand": "-", "sequence": "TCAGGACGCCGGCGATGAGCCGTCGTCCCAGCCGCCCAGCGCCTTGTACAGATCCACCGCGTTGACCAGCCGGCGCTGCTGCAGCCGGATGAATTCCTGTTCCGACTCGAACAGGCTGCGCTGGGCCTCCAGCATCTCCAGGTAGTTCGCCACCCCGCGCGCATAACGCCGCTCGGCCAGCCGCTGGCGTTCGCGGTCGGCGTCGCGCACCTTGCGCTGGGCCTCGATCTGGTCGCGCAGCGCGTCGCGCGCCGACAGCGCGTCGGCCACGTCGCGGAACGCGGCCTGGATGCTGCCTTCGTACTGGGCCACCGCGATGTGCTTGCGGGTCTCGGCCAGCGACAGGTTGGCGCGGTTGCGGCCGGCGTTGAAGATCGGCAGCGTCAGGCGCGGCGCGAAGCTCCAGCCGCCGGTGCCGCCGCTGAACAGATCCGAGAAGCGGTCGGCGGTGGTGCCGATGTCCGTGGTCAGCTGCACCGACGGGAAGAACGCCGCGCGCGCCGCGCCGATGTCGGCGTTGGCCGCGCGCAGCGCCTGCTCTGCCTGGCGCAGGTCGGGGCGGCGCGTCAGCAGTTCGGACGGCAGCCCCGCCGCCAGCGGCGTCAGGCTCTGGCTTTCCAGCGGCGTAGGGTCGACGCCGAGCGGCAGCGCGAAATCGCCGGCCAGCAGGCCCAGCGCGTGCCGCGCCAGGCTGGCCTCGCGGGTCAGCTCGGCGCGCGTGGCGCGCGAGCTTTCCACCAGCATCTGCGCGGTGCGCAGGCCGATGGCGGTTTCCAGCCCGGCGTCGTAGCGGCGCTGGGTCAGCTTGAGCGTGGTCTCGCGCAGCGCCAGCGTGTCGTCGGTCAGGCGCAGTTGCTCGGCCAGCGAACGCTGGTTGAAGTAGGCCGTCGCCGTCTCCGCCACCAGCGCCAGCGTGGCGGCGCGGTGCGCTTCCTCGCTGGCCAGGTAGCGCGCCAGCGCGGCGTCCGACAGGCTCCGCACCCGGCCGAAGAAGTCCAGCTCGAACGCGGTGATGCCGACGGCCGCGCGGTAGCGGTTGGACACCGGCGTGCGCGGCTGGCCCGGCTCGGTCGCGCGGCCGCGGCTGAATTCGCCGCTGGCGTCGATGGCCGGCAGGCGTTCGGATTGCTGCACGCCGTACAGCGCGCGCGCTTCCTCGATGCGCAGCGCCGCCACGCGCAGGTCGCGGTTGTTGGCCAGCGCGGCCGCGATCCAGGCCTGCAGCGCCGGATCGTTGAAATAGGCGCGCCAGTCCTGCGGCGCGGCGGCCTGGCCGGGCTGCGCCGGCGTGTCGTACTGCGCCGGCACCGGCGCCGCGGGGCGCTCATGGGTGGGCGCCAGCGAGCAGCCGGACAATGCCAGCGCCAGCAGGGTCATTGCCACGGGTTTCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter insuavis AXX-A", "NCBI_taxonomy_id": "1003200", "NCBI_taxonomy_cvterm_id": "41271"}, "protein_sequence": {"accession": "EGP45230", "sequence": "MKPVAMTLLALALSGCSLAPTHERPAAPVPAQYDTPAQPGQAAAPQDWRAYFNDPALQAWIAAALANNRDLRVAALRIEEARALYGVQQSERLPAIDASGEFSRGRATEPGQPRTPVSNRYRAAVGITAFELDFFGRVRSLSDAALARYLASEEAHRAATLALVAETATAYFNQRSLAEQLRLTDDTLALRETTLKLTQRRYDAGLETAIGLRTAQMLVESSRATRAELTREASLARHALGLLAGDFALPLGVDPTPLESQSLTPLAAGLPSELLTRRPDLRQAEQALRAANADIGAARAAFFPSVQLTTDIGTTADRFSDLFSGGTGGWSFAPRLTLPIFNAGRNRANLSLAETRKHIAVAQYEGSIQAAFRDVADALSARDALRDQIEAQRKVRDADRERQRLAERRYARGVANYLEMLEAQRSLFESEQEFIRLQQRRLVNAVDLYKALGGWDDGSSPAS"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "OprZ", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41270", "model_name": "OprZ", "model_type_id": "40292"}, "2797": {"model_id": "2797", "ARO_accession": "3004143", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "AxyX is the inner membrane transporter of the AxyXY-OprZ efflux pump system in Achromobacter spp.", "model_sequences": {"sequence": {"4133": {"dna_sequence": {"fmax": "28306", "fmin": "27130", "accession": "AFRQ01000061.1", "strand": "-", "sequence": "TTACCTTTTTTCGTTATTTCCCGCGGTCGCCACGGGCGCGCTCGGCGCGGTCCGCTCGACCGGTTTGATTTTCTGGCCGGGGGCCAGCTGCGCGGCGTTTTCCACCACCACGCGTTCGCCGCCCGCCAGGCCCTCGGTGACGACCCAGTTCGGGCCCAGCAGCCGGTGCGCGGTCACCGCCACGCTGCGCAGCTCGCCGTCGTCGCCGGCCACCAGCACGTGCGCGCCGTCGGCGTTGCGCAGCAGGGCGTTGCGCGGCACCAGGAAGGTGTCGCGGTTGACCGCCTGCTCCAGCCGCACCCGCACGTACATGCCCGGCAACAGTTCGCGGCCCGGGTTGGCGAACAGCGCGCGCATGGTCACGTTGTCGGTGCCGGGGTCGACCGCCAGGTCGGCGAACGACAGCGTGCCGCCCTGGCCATACTCGGAGCCGTCCGGCAGCAGCAGGCGCACCCGCATCTTGTCGGGCGCGACGCCTTGCAGGGCGCCGGCGCGGATCTGCTTCTGCAACTGCATGACCTCGGCCGCGGGTTGCGAGAAGTTGACGTAGATCGGGTCGAGTTGCTGCACCACCGTCAGCGGCGTGGCCTGGCCTTCGCCCACCAGCGCGCCCTCGGTGACCAGCGCGCGGCGCGCGCGGCCGTCGATCGGCGAGGTGACGCGGGCGTATTCCAGCCGCAGCCTGGCGCTCTGCAGGTTGGCCTTGGCCAACGCCACTTCGGCGCGGGCCTGGCGTTCCTGGGCCACGCTCTCGGCGTGGTCGCGTTCGCTGATGGCGCGGTCCGACACCAGGTCGGCGTAGCGGCGCAGCTTGTCGGCGGCGGCCGACAGGTTGGCCTGGGCACGCGCCAACGCGGCCGCCTCGGAATCGTAGGCCGCCTGCAGCGGCGCCGGATCGATCTGGAACAGCGGCGTGCCGCGCGTCACTTCCTGGCCTTCTTCATACAGGCGGCGGGTGACGATGCCGGCCACGCGGGCGCGGACCTCGGCCTCGCGATAGGGCTCCAGCCGGCCGGGCAGCTCGCTGGCGACGGCGGTGGGCGTGGCCCTGGCCACGATGACGCCGACTTCGGCGGGGGCCTTGGCGGCTTCGGGGGCTTCCTGCTTCGAGCATGCGGAAACGAGAACCAGTACGGATGCGAATGCGAGCGTTCTGAAGGGAACTCGGTGCGTCAT"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter insuavis AXX-A", "NCBI_taxonomy_id": "1003200", "NCBI_taxonomy_cvterm_id": "41271"}, "protein_sequence": {"accession": "EGP45232.2", "sequence": "MTHRVPFRTLAFASVLVLVSACSKQEAPEAAKAPAEVGVIVARATPTAVASELPGRLEPYREAEVRARVAGIVTRRLYEEGQEVTRGTPLFQIDPAPLQAAYDSEAAALARAQANLSAAADKLRRYADLVSDRAISERDHAESVAQERQARAEVALAKANLQSARLRLEYARVTSPIDGRARRALVTEGALVGEGQATPLTVVQQLDPIYVNFSQPAAEVMQLQKQIRAGALQGVAPDKMRVRLLLPDGSEYGQGGTLSFADLAVDPGTDNVTMRALFANPGRELLPGMYVRVRLEQAVNRDTFLVPRNALLRNADGAHVLVAGDDGELRSVAVTAHRLLGPNWVVTEGLAGGERVVVENAAQLAPGQKIKPVERTAPSAPVATAGNNEKR"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "AxyX", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41272", "model_name": "AxyX", "model_type_id": "40292"}, "2758": {"model_id": "2758", "ARO_accession": "3004099", "model_param": {"blastp_bit_score": {"param_value": "680", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LpeA is a subunit of the LpeAB efflux pump in Legionella pneumophila, which is homologous to AcrA in E. coli.", "model_sequences": {"sequence": {"4077": {"dna_sequence": {"fmax": "3281861", "fmin": "3280793", "accession": "CR628336.1", "strand": "+", "sequence": "GTGTTAGGAATTCAATTCAATAGAGGTCAATGGCGGTCAAACTATTATTGGCAAATACCTGTGCTGATAATAGCTGTTATTAGCATTCTGTTTTTCATCAGTAAAAAATTATTCTACTCAAAAGTTACGCCAGAAAGCATACCTAATAAACTGGTGGAAGTTGAGCCCATTAAAAGCCACAACTTACAACAAACAATCCATTTATTAGGTACCATTCATCCAAAACACGCAACGACATTAATTGCTAAAGAATCAGGTATGTTGGACACCCTTATCCCAACTGGTCAAAAAGTCACAAAAGGGACACTTATTGCAAAAATCAACAACCCTGATCTTGAAAAAAATCTACAGCTTTCATTAAGTGCGGTAGAATTGGCAAAAGCACAATATGAACGTATCACCCCTTTAATTAAATCAGGATATGTCAGTACAAAGGAAGTCGAAGAAAAAAAACAAGCCTGGATTGATGCCCAAAAAGAATTATCAAAAACAAGGATTGAATTAGATAACCTCCGCTTTTACGCTCCTTTCGACGGAATAATTGGAGCATACAAAAAGAGAGAAGGAGCACAAGTCAATGCAGGTGAATCTGTTGTAAGTATTTACGACCCTTCTGCTTTAGTTGTCGATTTTGATATTCCTTGCAGTAATTTGGCAACTCTTAATGAAGGTCAGCCGGTTTATGTGCTGGGTAAACGGTATTCATTAAGTCATTTACAAAAAATGCTCGACGAAGACACCCACATGTGCCCTGCTGATGTTGATATTCAATGTGATGATTGTCTTATTGGTGCGACCACAAGTGTTGAGCTCCTTGTTGCGGAAAAAAATAACACTATTGTCATCCCCTTCCAGGCAATATTTTTGAGAAATAGTAAACCTTTTGTATATCTTGTAAAAAAGGGAAAGATTGTGCTTGCTTCAGTGAAAACTGGGTTGCAACAAGAGGATAAAATTGAAATTGTCGAGGGATTAAAAGCTGGGCAACAACTGGTTACAAAAGGCCAGGAACGCTTATATCCTGAAATGACCGTTGATATTTATCATCCAGCGACAAGTAGCAGCTAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Legionella pneumophila str. Paris", "NCBI_taxonomy_id": "297246", "NCBI_taxonomy_cvterm_id": "41208"}, "protein_sequence": {"accession": "CAH14032.1", "sequence": "MLGIQFNRGQWRSNYYWQIPVLIIAVISILFFISKKLFYSKVTPESIPNKLVEVEPIKSHNLQQTIHLLGTIHPKHATTLIAKESGMLDTLIPTGQKVTKGTLIAKINNPDLEKNLQLSLSAVELAKAQYERITPLIKSGYVSTKEVEEKKQAWIDAQKELSKTRIELDNLRFYAPFDGIIGAYKKREGAQVNAGESVVSIYDPSALVVDFDIPCSNLATLNEGQPVYVLGKRYSLSHLQKMLDEDTHMCPADVDIQCDDCLIGATTSVELLVAEKNNTIVIPFQAIFLRNSKPFVYLVKKGKIVLASVKTGLQQEDKIEIVEGLKAGQQLVTKGQERLYPEMTVDIYHPATSSS"}}}}, "ARO_category": {"36298": {"category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_cvterm_id": "36298", "category_aro_accession": "3000159", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance."}}, "ARO_name": "LpeA", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41207", "model_name": "LpeA", "model_type_id": "40292"}, "2795": {"model_id": "2795", "ARO_accession": "3004139", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bitscore parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "MCR-3 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting reduction in negative charge of the cell membrane. Originally described by Yin et al. 2017, from a porcine Escherichia coli plasmid pWJ1.", "model_sequences": {"sequence": {"4121": {"dna_sequence": {"fmax": "162759", "fmin": "161133", "accession": "KY924928.1", "strand": "+", "sequence": "ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "ASF81896.1", "sequence": "MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"}}}}, "ARO_category": {"39418": {"category_aro_name": "determinant of polymyxin resistance", "category_aro_cvterm_id": "39418", "category_aro_accession": "3002984", "category_aro_description": "Enzymes, other proteins or other gene products shown clinically to confer resistance to polymyxin antibiotics, i.e. colistin."}, "40190": {"category_aro_name": "gene altering cell wall charge", "category_aro_cvterm_id": "40190", "category_aro_accession": "3003580", "category_aro_description": "Genes involved in alteration of the cell wall overall charge, leading to antimicrobial resistance due to reduced binding"}}, "ARO_name": "MCR-3", "model_type": "protein homolog model", "model_description": "Protein homolog models detect protein sequences based on their similarity to curated reference sequence, using curated BLASTP cut-offs. CARD cut-offs are currently based on BLAST bitscore cutoffs as they are independent of database size and query length.", "ARO_id": "41267", "model_name": "MCR-3", "model_type_id": "40292"}}}