{"$update": {"344": {"$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