{"$insert": {"3716": {"model_id": "3716", "model_name": "Mycobacterium tuberculosis Rv0191 mutations confer resistance to pyrazinamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9723": "V179A", "9724": "A213T"}, "clinical": {"9723": "V179A", "9724": "A213T"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "710"}}, "model_sequences": {"sequence": {"8775": {"protein_sequence": {"accession": "NP_214705.1", "sequence": "MTAPTGTSATTTRPWTPRIATQLSVLACAAFIYVTAEILPVGALSAIARNLRVSVVLVGTLLSWYALVAAVTTVPLVRWTAHWPRRRALVVSLVCLTVSQLVSALAPNFAVLAAGRVLCAVTHGLLWAVIAPIATRLVPPSHAGRATTSIYIGTSLALVVGSPLTAAMSLMWGWRLAAVCVTGAAAAVALAARLALPEMVLRADQLEHVGRRARHHRNPRLVKVSVLTMIAVTGHFVSYTYIVVIIRDVVGVRGPNLAWLLAAYGVAGLVSVPLVARPLDRWPKGAVIVGMTGLTAAFTLLTALAFGERHTAATALLGTGAIVLWGALATAVSPMLQSAAMRSGGDDPDGASGLYVTAFQIGIMAGALLGGLLYERSLAMMLTASAGLMGVALFGMTVSQHLFENPTLSPGDG"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "222288", "fmax": "223530", "strand": "+", "sequence": "ATGACTGCCCCAACCGGAACCTCCGCCACTACGACGCGACCGTGGACGCCACGGATCGCCACGCAACTGTCCGTGCTGGCTTGCGCGGCCTTTATCTATGTCACCGCCGAAATCCTGCCAGTGGGCGCGCTGTCGGCGATAGCGCGGAACTTGCGCGTCAGCGTGGTCCTAGTTGGGACCTTGCTGTCCTGGTATGCCCTTGTCGCGGCCGTGACAACGGTTCCGCTGGTGCGTTGGACCGCACACTGGCCGCGCCGCCGGGCCCTGGTGGTCAGCCTGGTCTGCCTGACCGTCTCGCAACTCGTCTCGGCGCTGGCGCCCAACTTCGCGGTGCTGGCCGCCGGGCGGGTGCTCTGCGCGGTCACCCATGGCCTGCTGTGGGCGGTCATCGCGCCGATCGCCACCCGGCTGGTGCCGCCCAGTCACGCCGGGCGCGCCACGACGTCGATCTACATCGGAACCAGTCTGGCGCTGGTCGTCGGTAGCCCACTCACGGCTGCCATGAGCCTGATGTGGGGTTGGCGGCTGGCGGCGGTGTGCGTGACCGGCGCGGCGGCCGCGGTCGCCCTGGCCGCCCGGCTGGCGTTGCCGGAGATGGTGCTGCGCGCCGACCAGCTCGAGCACGTTGGCCGACGGGCTCGTCACCACCGTAATCCTCGCCTGGTCAAGGTCAGTGTGCTCACGATGATCGCGGTAACCGGCCATTTCGTGTCCTACACCTACATCGTGGTGATCATCCGCGACGTCGTCGGTGTACGTGGGCCGAATCTGGCCTGGCTGCTCGCCGCCTATGGGGTCGCCGGCCTGGTGTCCGTGCCCCTGGTGGCGCGGCCGTTGGACCGTTGGCCCAAGGGCGCCGTCATCGTCGGTATGACCGGACTGACGGCGGCGTTCACCTTGCTGACCGCGCTGGCATTCGGTGAACGCCACACCGCGGCGACGGCACTGCTGGGCACCGGTGCGATTGTGCTGTGGGGAGCCTTGGCCACTGCCGTGTCACCGATGCTGCAATCGGCGGCGATGCGTAGCGGCGGCGACGACCCCGACGGGGCCTCAGGTTTGTATGTGACGGCGTTTCAGATCGGCATCATGGCCGGCGCTCTGCTGGGTGGGCTGCTCTACGAGCGCAGCTTGGCGATGATGCTGACCGCGTCGGCGGGTTTGATGGGTGTTGCGTTGTTCGGGATGACGGTTAGCCAGCACTTGTTCGAGAATCCGACTCTGAGTCCCGGCGACGGCTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004981", "ARO_id": "43168", "ARO_name": "Mycobacterium tuberculosis Rv0191 mutations confer resistance to pyrazinamide", "CARD_short_name": "Mtub_Rv0191_PZA", "ARO_description": "Mutations in the Rv0191 gene contribute to or confer resistance to pyrazinamide.", "ARO_category": {"43167": {"category_aro_accession": "3004980", "category_aro_cvterm_id": "43167", "category_aro_name": "pyrazinamide resistant Rv0191", "category_aro_description": "A probable conserved integral membrane protein that acts as an active efflux pump. Overexpression causes pyrazinamide resistance.", "category_aro_class_name": "AMR Gene Family"}, "39997": {"category_aro_accession": "3003413", "category_aro_cvterm_id": "39997", "category_aro_name": "pyrazinamide", "category_aro_description": "Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.", "category_aro_class_name": "Antibiotic"}, "45737": {"category_aro_accession": "3007155", "category_aro_cvterm_id": "45737", "category_aro_name": "pyrazine antibiotic", "category_aro_description": "A group of antibiotics derived from pyrazine.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3726": {"model_id": "3726", "model_name": "Mycobacterium tuberculosis inbR mutations conferring resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"12576": "R9H", "12578": "L17Q"}, "clinical": {"12576": "R9H", "12578": "L17Q"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "400"}}, "model_sequences": {"sequence": {"8773": {"protein_sequence": {"accession": "YP_177706.1", "sequence": "MTRSDRPYRGVEAAERLATRRRQSLSAGLDLLGSDQHDIAELTIRTICRRAGLSVRYFYESFTDKDEFVGRVFDWVVAELVATTQAAVTAVPAREQTRAGMANIVRTITADARVGRLLFSTQLANAVITRKRAESSALFAMLSGQHAVDTLHAPANDHVKAVAHFAVGGVGQTISAWLAGDVRLDPDQLVDQLAALLDELTDPNLSRPRVAATAAKSGANDPQPPEVAGQPPSSARPARRS"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "330932", "fmax": "331658", "strand": "-", "sequence": "ATGACGCGCAGTGATCGACCCTACCGCGGCGTCGAGGCCGCCGAGCGACTGGCGACGCGCCGTCGCCAGTCGCTCTCTGCCGGCCTGGACCTGTTGGGGTCCGACCAGCACGACATCGCCGAGCTAACCATCCGCACCATTTGCCGGCGGGCCGGCCTGTCGGTGCGCTACTTCTACGAAAGCTTCACCGACAAGGACGAATTCGTCGGCCGCGTGTTCGACTGGGTGGTGGCCGAGCTGGTCGCCACCACTCAGGCCGCGGTCACGGCGGTACCGGCGCGGGAGCAGACTCGCGCGGGCATGGCCAACATCGTGCGGACCATCACCGCAGACGCCCGCGTCGGACGCCTGCTGTTCAGCACACAGCTGGCCAACGCAGTGATCACCCGCAAGCGTGCGGAATCCAGCGCCCTGTTCGCCATGCTGTCCGGCCAACATGCCGTCGACACCCTGCACGCACCGGCAAATGACCACGTCAAGGCGGTCGCACACTTCGCCGTCGGCGGCGTCGGGCAGACCATCAGCGCCTGGCTGGCCGGTGACGTGCGACTCGATCCCGACCAGCTGGTCGATCAGCTAGCTGCGCTGCTCGATGAACTCACCGACCCAAACTTGTCCCGTCCCCGGGTAGCGGCAACAGCTGCCAAATCCGGGGCTAACGATCCGCAGCCACCGGAGGTCGCCGGTCAGCCGCCGTCTTCGGCACGGCCTGCGCGTCGCTCGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004924", "ARO_id": "43110", "ARO_name": "Mycobacterium tuberculosis inbR mutations conferring resistance to isoniazid", "CARD_short_name": "Mtub_inbR_INH", "ARO_description": "Mutations that occur in inbR that result in or contribute to antibiotic resistance to isoniazid.", "ARO_category": {"43085": {"category_aro_accession": "3004899", "category_aro_cvterm_id": "43085", "category_aro_name": "isoniazid resistant inbR", "category_aro_description": "inbR is part of the transcriptional factor family TetR. It acts as a repressor to regulate efflux pumps involved in antibiotic resistance.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3718": {"model_id": "3718", "model_name": "Mycobacterium tuberculosis Rv2731 mutations confer resistance to pyrazinamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9731": "P82T", "9732": "F89L"}, "clinical": {"9731": "P82T", "9732": "F89L"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "800"}}, "model_sequences": {"sequence": {"8781": {"protein_sequence": {"accession": "NP_217247.1", "sequence": "MTADEPRSDDSSGSAPQPAATPVPRPGPRPGPRPVPRPTSYPVGAHPPSDPHRFGRIDDDGTVWLVSASGERIVGSWQAGDPEAAFAHFGRRFDDLSTEIMLMDERLASGTGDARKIKAHAIALAETLPTACVLGDVDALADRLTSIRDRAEVIAAADRSRREEHRAAQTARKEALAAEAEELAANATQWKVAGDRLRAILDEWKTISGVDRKVDDALWKRYSTARDTFNRRRGSHFAELDRERSGVRQSKERLCERAEELSESTDWTATSAEFRKLLADWKAAGRASKDVDDALWRRFKAAQDSFFTARNAATAEKEAELRANADAKEALLAEAERLDTTNHEAARAALRSIAEKWDAIGKVSRERAAELERRLRAVEKKVREAGEADWSDPQARARAEQFRARAEQFEHQAEKAAAAGRTKEADEAKANAEQWRQWAEAAADALTRRP"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3043025", "fmax": "3044378", "strand": "+", "sequence": "ATGACGGCCGACGAGCCCCGCAGCGACGATTCGTCCGGGTCGGCCCCCCAACCGGCTGCCACGCCGGTGCCCCGCCCGGGACCGCGTCCCGGCCCCCGGCCGGTGCCGCGACCCACCTCCTACCCGGTGGGTGCGCACCCTCCCAGCGACCCGCACCGTTTCGGCCGTATCGACGACGACGGCACGGTGTGGCTGGTCAGTGCGAGCGGCGAGCGTATCGTCGGCTCCTGGCAGGCCGGCGATCCCGAAGCCGCGTTTGCCCATTTCGGCAGGCGATTCGATGACCTGAGCACCGAAATCATGCTGATGGACGAGCGGTTGGCGTCCGGCACCGGCGACGCACGCAAGATCAAAGCCCATGCGATCGCGCTGGCCGAAACGTTGCCGACGGCATGCGTGCTGGGCGATGTCGACGCGCTGGCAGACCGGTTGACAAGCATTCGTGATCGCGCGGAGGTCATCGCTGCCGCCGACCGCTCCAGACGCGAGGAACATCGAGCCGCCCAGACCGCCCGTAAAGAGGCGCTGGCCGCCGAAGCCGAGGAGCTGGCCGCCAACGCGACACAATGGAAGGTCGCCGGTGACCGGCTGCGGGCAATCCTCGATGAATGGAAGACGATTAGCGGTGTGGACCGCAAGGTCGATGACGCGCTGTGGAAGCGCTACTCGACGGCCCGCGATACGTTCAACCGGCGGCGAGGGTCCCACTTCGCCGAATTGGACCGTGAGCGATCCGGCGTCCGGCAAAGCAAGGAACGGCTTTGTGAACGGGCCGAGGAGTTGTCCGAGTCGACGGACTGGACCGCCACCAGCGCGGAGTTCCGCAAGCTGCTCGCCGACTGGAAAGCGGCGGGACGCGCGAGCAAGGATGTGGACGACGCCCTGTGGCGTCGCTTCAAGGCCGCGCAGGACTCCTTCTTCACGGCTCGCAATGCCGCCACCGCCGAGAAGGAGGCCGAGTTGCGAGCCAATGCCGACGCCAAGGAGGCGCTGCTGGCCGAAGCGGAGCGGCTCGACACGACAAACCACGAGGCCGCTCGAGCAGCGCTGCGGTCGATCGCCGAGAAGTGGGACGCGATCGGCAAGGTGTCGCGGGAGCGGGCCGCGGAGCTGGAGCGGCGACTACGCGCGGTCGAGAAAAAGGTGCGAGAAGCCGGCGAAGCGGATTGGTCCGACCCGCAGGCGCGGGCCCGCGCCGAGCAGTTCCGCGCCCGGGCCGAGCAGTTTGAACACCAGGCCGAGAAGGCAGCAGCGGCCGGTCGCACCAAGGAAGCCGACGAGGCGAAGGCGAACGCCGAACAATGGCGGCAGTGGGCCGAGGCAGCCGCCGACGCGTTGACCCGACGCCCCTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004987", "ARO_id": "43174", "ARO_name": "Mycobacterium tuberculosis Rv2731 mutations confer resistance to pyrazinamide", "CARD_short_name": "Mtub_Rv2731_PZA", "ARO_description": "Mutations in the Rv2731 gene that contribute to or confer resistance to pyrazinamide.", "ARO_category": {"43173": {"category_aro_accession": "3004986", "category_aro_cvterm_id": "43173", "category_aro_name": "pyrazinamide resistant Rv2731", "category_aro_description": "A conserved alanine and arginine-rich protein with an unknown function. The protein has shown to contribute to or confer resistance to pyrazinamide.", "category_aro_class_name": "AMR Gene Family"}, "39997": {"category_aro_accession": "3003413", "category_aro_cvterm_id": "39997", "category_aro_name": "pyrazinamide", "category_aro_description": "Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.", "category_aro_class_name": "Antibiotic"}, "45737": {"category_aro_accession": "3007155", "category_aro_cvterm_id": "45737", "category_aro_name": "pyrazine antibiotic", "category_aro_description": "A group of antibiotics derived from pyrazine.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3729": {"model_id": "3729", "model_name": "Mycobacterium tuberculosis mshC mutations conferring resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9566": "A403G"}, "clinical": {"9566": "A403G"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "775"}}, "model_sequences": {"sequence": {"8839": {"protein_sequence": {"accession": "NP_216646.1", "sequence": "MQSWYCPPVPVLPGRGPQLRLYDSADRQVRPVAPGSKATMYVCGITPYDATHLGHAATYVTFDLIHRLWLDLGHELHYVQNITDIDDPLFERADRDGVDWRDLAQAEVALFCEDMAALRVLPPQDYVGATEAIAEMVELIEKMLACGAAYVIDREMGEYQDIYFRADATLQFGYESGYDRDTMLRLCEERGGDPRRPGKSDELDALLWRAARPGEPSWPSPFGPGRPGWHVECAAIALSRIGSGLDIQGGGSDLIFPHHEFTAAHAECVSGERRFARHYVHAGMIGWDGHKMSKSRGNLVLVSALRAQDVEPSAVRLGLLAGHYRADRFWSQQVLDEATARLHRWRTATALPAGPAAVDVVARVRRYLADDLDTPKAIAALDGWVTDAVEYGGHDAGAPKLVATAIDALLGVDL"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "2391214", "fmax": "2392459", "strand": "-", "sequence": "ATGCAGTCGTGGTATTGCCCACCGGTTCCGGTGTTGCCGGGACGAGGCCCGCAGCTACGGCTGTACGACAGCGCCGACCGGCAGGTCCGTCCGGTGGCGCCCGGATCTAAGGCCACCATGTACGTCTGCGGGATCACGCCCTACGACGCCACGCATCTGGGCCATGCTGCCACCTATGTGACGTTCGACCTGATCCATCGGCTGTGGCTGGATCTCGGTCATGAATTGCACTATGTCCAGAACATCACCGACATCGACGATCCACTATTTGAGCGCGCGGATCGCGACGGTGTCGACTGGCGTGACCTTGCCCAAGCCGAGGTCGCCCTGTTCTGTGAGGACATGGCGGCGCTGCGGGTGCTACCACCGCAAGACTACGTGGGGGCCACCGAAGCGATTGCTGAAATGGTCGAGCTCATCGAAAAAATGCTGGCGTGCGGGGCGGCCTATGTCATAGACCGGGAAATGGGAGAGTACCAGGACATCTACTTCCGCGCTGACGCCACCCTGCAGTTCGGCTACGAGTCAGGGTATGACCGTGACACCATGCTGCGGCTGTGCGAGGAACGTGGCGGCGATCCGCGGCGCCCCGGCAAGAGCGACGAACTCGACGCGTTGTTGTGGCGGGCCGCGCGGCCCGGTGAGCCCAGCTGGCCGTCCCCGTTCGGGCCTGGCCGGCCAGGCTGGCATGTCGAGTGCGCAGCCATCGCGCTCAGTCGTATCGGAAGCGGCCTCGACATCCAGGGCGGTGGTAGCGATCTGATCTTTCCGCACCACGAGTTCACCGCTGCGCACGCCGAATGTGTCAGCGGCGAACGGCGATTCGCGCGGCACTACGTGCATGCCGGGATGATCGGCTGGGACGGGCACAAGATGTCAAAGAGCCGCGGCAACCTCGTGCTGGTGTCGGCGCTGCGTGCGCAGGACGTTGAGCCATCGGCGGTTCGGCTGGGTTTGCTCGCCGGACACTACCGAGCCGATCGGTTCTGGAGCCAGCAGGTGCTTGACGAGGCGACCGCCCGGCTGCACCGTTGGCGCACCGCAACCGCACTTCCCGCCGGTCCGGCCGCAGTTGACGTTGTCGCTCGGGTGCGCCGCTACCTGGCCGACGATCTCGATACGCCCAAAGCGATTGCCGCACTGGATGGTTGGGTCACCGATGCGGTGGAGTACGGCGGCCACGATGCCGGGGCGCCGAAGTTGGTGGCGACGGCGATCGATGCCCTGCTCGGGGTGGACCTGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004927", "ARO_id": "43113", "ARO_name": "Mycobacterium tuberculosis mshC mutations conferring resistance to isoniazid", "CARD_short_name": "Mtub_mshC_INH", "ARO_description": "Mutations that occur in mshC that result in or contribute to antibiotic resistance to isoniazid.", "ARO_category": {"43090": {"category_aro_accession": "3004904", "category_aro_cvterm_id": "43090", "category_aro_name": "isoniazid resistant mshC", "category_aro_description": "Mutations that occur on the mshC gene resulting in the inability for isoniazid to function. It catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3720": {"model_id": "3720", "model_name": "Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"40394": {"param_type": "nonsense mutation", "param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a stop codon, encoded as [wild type amino acid][position][Ter], for example Q42Ter.", "param_type_id": "40394", "param_value": {"9733": "Y53Ter"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9734": "N56S", "9735": "W171R", "9737": "A194P", "9736": "A190G"}, "clinical": {"9734": "N56S", "9735": "W171R", "9737": "A194P", "9736": "A190G"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "680"}}, "model_sequences": {"sequence": {"8783": {"protein_sequence": {"accession": "NP_217685.1", "sequence": "MPQMLGPLDEYPLHQLPQPIAWPGSSDRNFYDRSYFNAHDRTGNIFLITGIGYYPNLGVKDAFVLIRRADIQTAVHLSDAIDSDRLHQHVNGYRVEVVEPLRKLRIVLDETEGVAADLTWEGLFDVVQEQPHVLRSGNRVTLDAQRFAQLGTWSGRIVVDGERIAVDPATWLGSRDRSWGIRPVGEPEPAGRPADPPFEGMWWLYVPLAFDDFAVVLIIQEEPDGFRSLNDCTRIWRDGHVEQLGWPRVRIHYRSGTRIPTGATIEASTPDGAPVHFDVESKLAVPTHVGGGYGGDSDWSHGMWKGEKFVERRTYDMTDPTIIARAGFGVIDHVGRALCRDGDGNPVQGWGLFEHGALGRHDPSGFADWSTLAP"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3537237", "fmax": "3538362", "strand": "+", "sequence": "ATGCCGCAAATGCTAGGCCCACTCGACGAGTACCCGCTACATCAGCTTCCCCAGCCGATCGCCTGGCCGGGCTCCTCCGACCGCAACTTCTACGACCGCTCCTACTTCAACGCCCACGACCGCACCGGGAACATCTTTCTGATCACCGGTATCGGCTACTACCCTAACCTGGGCGTGAAAGACGCGTTCGTGCTGATCAGGCGTGCGGACATACAGACCGCGGTGCATCTTTCGGATGCCATCGACTCCGACCGGCTACACCAGCACGTCAACGGTTACCGGGTGGAGGTCGTCGAGCCGCTGCGAAAACTGCGTATCGTGCTCGACGAAACCGAAGGTGTGGCGGCCGATCTCACCTGGGAGGGCCTGTTCGACGTCGTCCAGGAACAGCCGCACGTCTTGCGCTCCGGCAACCGGGTGACCCTGGATGCGCAGCGCTTCGCGCAGCTGGGCACCTGGAGCGGCCGCATCGTCGTCGACGGCGAACGGATCGCCGTCGATCCGGCGACCTGGCTCGGCAGCCGGGACCGGTCCTGGGGCATCCGGCCGGTGGGGGAACCAGAACCGGCGGGCCGGCCCGCCGACCCACCCTTCGAGGGCATGTGGTGGCTGTATGTGCCGTTGGCCTTCGACGACTTCGCCGTCGTGCTGATCATCCAGGAAGAACCCGACGGGTTCCGCTCGCTCAACGACTGCACCCGGATCTGGCGTGACGGCCACGTCGAGCAGCTGGGCTGGCCGCGGGTGCGGATCCACTACCGCTCCGGCACCCGCATCCCGACCGGGGCGACGATCGAGGCAAGCACCCCCGACGGCGCGCCGGTGCACTTCGACGTGGAGTCCAAACTGGCGGTGCCGACCCATGTCGGTGGCGGCTACGGGGGTGACTCGGACTGGTCACATGGCATGTGGAAGGGCGAGAAGTTCGTCGAGCGAAGAACCTACGACATGACCGATCCGACGATCATCGCGCGGGCCGGCTTCGGCGTCATCGACCACGTCGGTCGCGCGCTATGCCGCGACGGCGACGGGAATCCAGTGCAGGGCTGGGGTCTGTTTGAACACGGGGCGCTGGGCCGCCACGACCCATCGGGGTTCGCCGACTGGTCTACGCTGGCGCCCTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004993", "ARO_id": "43180", "ARO_name": "Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide", "CARD_short_name": "Mtub_Rv3169_PZA", "ARO_description": "Mutations in the Rv3169 gene that can contribute to or confer resistance to pyrazinamide resistance.", "ARO_category": {"43179": {"category_aro_accession": "3004992", "category_aro_cvterm_id": "43179", "category_aro_name": "pyrazinamide resistant Rv3169", "category_aro_description": "A conserved protein with an unknown function determined through proteomics study. May contribute or confer resistance to pyrazinamide resistance.", "category_aro_class_name": "AMR Gene Family"}, "39997": {"category_aro_accession": "3003413", "category_aro_cvterm_id": "39997", "category_aro_name": "pyrazinamide", "category_aro_description": "Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.", "category_aro_class_name": "Antibiotic"}, "45737": {"category_aro_accession": "3007155", "category_aro_cvterm_id": "45737", "category_aro_name": "pyrazine antibiotic", "category_aro_description": "A group of antibiotics derived from pyrazine.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3731": {"model_id": "3731", "model_name": "Mycobacterium tuberculosis mymA mutations conferring resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"40394": {"param_type": "nonsense mutation", "param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a stop codon, encoded as [wild type amino acid][position][Ter], for example Q42Ter.", "param_type_id": "40394", "param_value": {"9575": "W271Ter"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9569": "M371I", "9574": "A205T"}, "clinical": {"9569": "M371I", "9574": "A205T"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "980"}}, "model_sequences": {"sequence": {"6033": {"protein_sequence": {"accession": "NP_217599.1", "sequence": "MNQHFDVLIIGAGLSGIGTACHVTAEFPDKTIALLERRERLGGTWDLFRYPGVRSDSDMFTFGYKFRPWRDVKVLADGASIRQYIADTATEFGVDEKIHYGLKVNTAEWSSRQCRWTVAGVHEATGETRTYTCDYLISCTGYYNYDAGYLPDFPGVHRFGGRCVHPQHWPEDLDYSGKKVVVIGSGATAVTLVPAMAGSNPGSAAHVTMLQRSPSYIFSLPAVDKISEVLGRFLPDRWVYEFGRRRNIAIQRKLYQACRRWPKLMRRLLLWEVRRRLGRSVDMSNFTPNYLPWDERLCAVPNGDLFKTLASGAASVVTDQIETFTEKGILCKSGREIEADIIVTATGLNIQMLGGMRLIVDGAEYQLPEKMTYKGVLLENAPNLAWIIGYTNASWTLKSDIAGAYLCRLLRHMADNGYTVATPRDAQDCALDVGMFDQLNSGYVKRGQDIMPRQGSKHPWRVLMHYEKDAKILLEDPIDDGVLHFAAAAQDHAAA"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3448503", "fmax": "3449991", "strand": "+", "sequence": "ATGAACCAGCATTTCGACGTCCTGATCATCGGCGCCGGCCTATCCGGCATCGGGACGGCCTGTCACGTGACGGCCGAGTTCCCCGACAAGACAATCGCCCTCCTGGAACGACGGGAGCGCCTGGGCGGCACCTGGGACTTGTTCCGCTACCCGGGAGTTCGTTCGGACTCCGACATGTTCACCTTCGGCTACAAGTTCCGCCCGTGGCGCGACGTGAAGGTGCTCGCCGACGGCGCGTCGATCCGGCAGTACATCGCCGACACCGCCACGGAGTTCGGCGTCGACGAGAAGATTCACTACGGCCTGAAGGTCAACACCGCCGAGTGGTCGAGCCGGCAGTGCCGTTGGACCGTCGCGGGCGTGCACGAGGCGACCGGCGAAACCCGGACCTACACCTGCGATTACCTCATCAGCTGCACCGGCTACTACAACTACGACGCGGGTTATCTGCCGGACTTCCCCGGCGTGCACCGGTTCGGCGGCCGGTGCGTGCACCCGCAGCACTGGCCCGAAGACCTCGATTATTCCGGCAAGAAGGTCGTCGTCATCGGCAGCGGCGCAACGGCGGTCACTTTGGTTCCGGCGATGGCCGGCTCCAACCCCGGCAGTGCCGCGCACGTGACGATGCTGCAGCGATCCCCGTCGTACATCTTCTCGCTGCCGGCGGTCGACAAGATCTCCGAAGTCCTGGGCCGCTTCCTGCCGGATCGCTGGGTCTACGAGTTTGGCCGCAGGCGCAACATCGCCATCCAGCGAAAGCTCTACCAGGCCTGCCGGCGCTGGCCCAAGCTGATGCGGCGATTGCTGCTGTGGGAGGTACGACGCCGCCTCGGCCGCTCCGTGGACATGAGCAACTTCACCCCGAACTACCTGCCGTGGGACGAGCGGTTGTGCGCCGTGCCCAACGGCGATCTGTTTAAGACGCTGGCCTCGGGCGCGGCGTCGGTGGTGACCGATCAGATCGAGACCTTCACCGAGAAGGGCATCCTGTGCAAGTCCGGCCGGGAGATCGAGGCCGACATCATCGTCACCGCGACCGGTCTGAACATCCAGATGCTGGGCGGGATGCGACTCATCGTGGACGGCGCCGAATACCAGCTGCCGGAGAAGATGACCTATAAGGGTGTGCTGCTGGAAAACGCCCCCAATCTGGCCTGGATCATCGGCTACACCAACGCGTCATGGACCCTGAAGTCCGACATCGCCGGCGCCTACCTGTGCCGGCTGCTGCGGCACATGGCCGACAACGGCTACACGGTGGCAACGCCGCGCGATGCGCAGGACTGCGCGCTGGACGTTGGCATGTTCGACCAGCTGAACTCCGGCTATGTGAAGCGCGGCCAGGACATCATGCCGCGCCAGGGCTCCAAGCATCCGTGGAGGGTGCTCATGCACTACGAGAAGGACGCCAAGATCCTGCTCGAAGACCCCATCGATGACGGCGTGCTGCACTTCGCCGCAGCGGCCCAAGACCACGCGGCGGCCTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004928", "ARO_id": "43114", "ARO_name": "Mycobacterium tuberculosis mymA mutations conferring resistance to isoniazid", "CARD_short_name": "Mtub_mymA_INH", "ARO_description": "Mutations that occur in the mymA operon that result in or contribute to antibiotic resistance to isoniazid.", "ARO_category": {"43092": {"category_aro_accession": "3004906", "category_aro_cvterm_id": "43092", "category_aro_name": "isoniazid resistant mymA", "category_aro_description": "mymA is an operon that begins at Rv3083 and ends at Rv3089 and is required for maintaining the appropriate mycolic acid composition and permeability of the envelope on its exposure to acidic pH. It has shown to be resistant to isoniazid.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3707": {"model_id": "3707", "model_name": "Mycobacterium tuberculosis eis mutations confer resistance to kanamycin", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"41339": {"param_type": "snp in promoter region", "param_description": "A SNP in the promoter region of a gene which alters transcription of that gene, encoded as [wild-type][-][position][mutation], for example t-11c. Var represents any possible substitution. This is a pilot parameter in need of further documentation.", "param_type_id": "41339", "param_value": {"13284": "c-14t", "13328": "g-10a", "15412": "g-10a", "15413": "c-12t", "15414": "c-14t", "15415": "g-37t"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9594": "V163I", "13016": "C12T", "13017": "C14T", "13019": "G37T"}, "clinical": {"9594": "V163I", "13016": "C12T", "13017": "C14T", "13019": "G37T"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "725"}}, "model_sequences": {"sequence": {"8827": {"protein_sequence": {"accession": "NP_216932.2", "sequence": "MTVTLCSPTEDDWPGMFLLAAASFTDFIGPESATAWRTLVPTDGAVVVRDGAGPGSEVVGMALYMDLRLTVPGEVVLPTAGLSFVAVAPTHRRRGLLRAMCAELHRRIADSGYPVAALHASEGGIYGRFGYGPATTLHELTVDRRFARFHADAPGGGLGGSSVRLVRPTEHRGEFEAIYERWRQQVPGGLLRPQVLWDELLAECKAAPGGDRESFALLHPDGYALYRVDRTDLKLARVSELRAVTADAHCALWRALIGLDSMERISIITHPQDPLPHLLTDTRLARTTWRQDGLWLRIMNVPAALEARGYAHEVGEFSTVLEVSDGGRFALKIGDGRARCTPTDAAAEIEMDRDVLGSLYLGAHRASTLAAANRLRTKDSQLLRRLDAAFASDVPVQTAFEF"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "2714123", "fmax": "2715332", "strand": "-", "sequence": "GTGACTGTGACCCTGTGTAGCCCGACCGAGGACGACTGGCCGGGGATGTTCCTACTGGCCGCGGCCAGTTTCACCGATTTCATCGGCCCTGAATCAGCGACCGCCTGGCGGACCCTGGTGCCCACCGACGGAGCGGTGGTGGTCCGCGATGGTGCCGGCCCGGGTTCTGAGGTGGTCGGGATGGCGCTGTACATGGATCTGCGGTTGACGGTGCCTGGTGAAGTGGTGCTCCCGACCGCCGGTCTCAGTTTCGTCGCGGTGGCGCCGACGCATCGCCGGCGCGGCTTGCTGCGCGCGATGTGCGCCGAACTGCACCGCCGCATAGCCGATTCCGGCTATCCGGTCGCGGCACTGCATGCTAGCGAGGGCGGCATCTACGGCCGGTTCGGCTACGGGCCCGCTACCACCTTGCATGAGCTGACGGTCGACCGACGCTTCGCGCGCTTTCACGCCGACGCACCGGGCGGCGGCCTAGGTGGCAGCAGCGTCCGGTTGGTCAGACCCACCGAGCATCGCGGCGAGTTTGAGGCGATCTACGAGCGATGGCGCCAGCAGGTGCCGGGCGGGCTGCTACGCCCGCAGGTGCTCTGGGACGAGCTGCTGGCAGAATGCAAAGCCGCGCCCGGTGGAGACCGTGAATCGTTCGCGTTACTGCATCCCGACGGGTACGCGCTGTACCGGGTGGATCGCACCGATCTCAAGCTAGCGCGCGTCAGCGAACTCAGGGCGGTAACCGCAGATGCGCATTGTGCGTTGTGGCGGGCCCTGATTGGCCTCGACTCCATGGAGCGAATCAGCATCATCACCCATCCACAGGACCCGTTACCCCACCTGCTCACCGATACCCGACTGGCCCGCACTACCTGGCGCCAGGACGGCCTGTGGTTGCGCATCATGAACGTACCGGCCGCACTCGAGGCGCGTGGTTACGCTCACGAAGTTGGCGAGTTTTCCACGGTCCTCGAGGTATCCGATGGCGGCCGGTTCGCGCTCAAGATCGGTGACGGCCGTGCGCGGTGTACCCCGACCGATGCGGCAGCCGAGATCGAAATGGATCGGGACGTACTGGGCAGCCTTTACCTTGGAGCGCACCGCGCTTCGACGTTAGCCGCCGCTAACCGGTTGCGCACCAAAGATTCCCAGCTGCTTCGTCGACTCGACGCGGCGTTTGCCAGTGATGTTCCCGTCCAGACCGCGTTCGAGTTCTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004963", "ARO_id": "43149", "ARO_name": "Mycobacterium tuberculosis eis mutations confer resistance to kanamycin", "CARD_short_name": "Mtub_eis_KAN", "ARO_description": "Mutations in eis that contribute to or confer resistance to kanamycin.", "ARO_category": {"43148": {"category_aro_accession": "3004962", "category_aro_cvterm_id": "43148", "category_aro_name": "kanamycin resistant eis", "category_aro_description": "Involved in acetylation and intracellular survival. Associated with the cell surface and secretion proteins.", "category_aro_class_name": "AMR Gene Family"}, "35966": {"category_aro_accession": "0000049", "category_aro_cvterm_id": "35966", "category_aro_name": "kanamycin A", "category_aro_description": "Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.", "category_aro_class_name": "Antibiotic"}, "35935": {"category_aro_accession": "0000016", "category_aro_cvterm_id": "35935", "category_aro_name": "aminoglycoside antibiotic", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3702": {"model_id": "3702", "model_name": "Mycobacterium tuberculosis inhA mutations conferring resistance to ethionamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"14806": "S94A", "9515": "I194T", "9517": "I21T", "9516": "I21V"}, "clinical": {"14806": "S94A", "9515": "I194T", "9517": "I21T", "9516": "I21V"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"8774": {"protein_sequence": {"accession": "NP_216000.1", "sequence": "MTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "1674201", "fmax": "1675011", "strand": "+", "sequence": "ATGACAGGACTGCTGGACGGCAAACGGATTCTGGTTAGCGGAATCATCACCGACTCGTCGATCGCGTTTCACATCGCACGGGTAGCCCAGGAGCAGGGCGCCCAGCTGGTGCTCACCGGGTTCGACCGGCTGCGGCTGATTCAGCGCATCACCGACCGGCTGCCGGCAAAGGCCCCGCTGCTCGAACTCGACGTGCAAAACGAGGAGCACCTGGCCAGCTTGGCCGGCCGGGTGACCGAGGCGATCGGGGCGGGCAACAAGCTCGACGGGGTGGTGCATTCGATTGGGTTCATGCCGCAGACCGGGATGGGCATCAACCCGTTCTTCGACGCGCCCTACGCGGATGTGTCCAAGGGCATCCACATCTCGGCGTATTCGTATGCTTCGATGGCCAAGGCGCTGCTGCCGATCATGAACCCCGGAGGTTCCATCGTCGGCATGGACTTCGACCCGAGCCGGGCGATGCCGGCCTACAACTGGATGACGGTCGCCAAGAGCGCGTTGGAGTCGGTCAACAGGTTCGTGGCGCGCGAGGCCGGCAAGTACGGTGTGCGTTCGAATCTCGTTGCCGCAGGCCCTATCCGGACGCTGGCGATGAGTGCGATCGTCGGCGGTGCGCTCGGCGAGGAGGCCGGCGCCCAGATCCAGCTGCTCGAGGAGGGCTGGGATCAGCGCGCTCCGATCGGCTGGAACATGAAGGATGCGACGCCGGTCGCCAAGACGGTGTGCGCGCTGCTGTCTGACTGGCTGCCGGCGACCACGGGTGACATCATCTACGCCGACGGCGGCGCGCACACCCAATTGCTCTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004876", "ARO_id": "43062", "ARO_name": "Mycobacterium tuberculosis inhA mutations conferring resistance to ethionamide", "CARD_short_name": "Mtub_inhA_ETO", "ARO_description": "inhA is a enoyl-acyl carrier reductase used in lipid metabolism and farry acid biosynthesis. It is inhibited by ethionamide. Mutations in the promoter region or multiple copies of the inhA show marked resistance to ethionamide mediated inhibition of mycolic acid biosynthesis.", "ARO_category": {"43061": {"category_aro_accession": "3004875", "category_aro_cvterm_id": "43061", "category_aro_name": "inhA with mutations with conferring resistance to ethionamide", "category_aro_description": "Genes with mutations in inhA which confer resistance to ethionamide class antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "40067": {"category_aro_accession": "3003474", "category_aro_cvterm_id": "40067", "category_aro_name": "ethionamide", "category_aro_description": "Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.", "category_aro_class_name": "Antibiotic"}, "45738": {"category_aro_accession": "3007156", "category_aro_cvterm_id": "45738", "category_aro_name": "thioamide antibiotic", "category_aro_description": "A group of antibiotics possessing the thioamide functional group.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3703": {"model_id": "3703", "model_name": "Mycobacterium tuberculosis nudC mutations conferring resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9587": "S287N", "9590": "P239R"}, "clinical": {"9587": "S287N", "9590": "P239R"}}, "40494": {"param_type": "frameshift mutation", "param_description": "A frameshift mutation, caused by a nucleotide insertion or deletion that does not equal 3 bases, encoded as [wild-type][position]fs, for example S531fs. Termination can also be denoted as: Ter[position]fs.", "param_type_id": "40494", "param_value": {"9588": "A216fs"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "550"}}, "model_sequences": {"sequence": {"8784": {"protein_sequence": {"accession": "NP_217715.1", "sequence": "MTNVSGVDFQLRSVPLLSRVGADRADRLRTDMEAAAAGWPGAALLRVDSRNRVLVANGRVLLGAAIELADKPPPEAVFLGRVEGGRHVWAVRAALQPIADPDIPAEAVDLRGLGRIMDDTSSQLVSSASALLNWHDNARFSALDGAPTKPARAGWSRVNPITGHEEFPRIDPAVICLVHDGADRAVLARQAAWPERMFSLLAGFVEAGESFEVCVAREIREEIGLTVRDVRYLGSQQWPFPRSLMVGFHALGDPDEEFSFSDGEIAEAAWFTRDEVRAALAAGDWSSASESKLLLPGSISIARVIIESWAACE"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3571601", "fmax": "3572543", "strand": "-", "sequence": "GTGACGAACGTAAGCGGCGTGGATTTTCAGCTGAGAAGCGTTCCGTTGCTTTCGCGCGTCGGCGCCGACCGGGCCGACCGGCTGAGGACCGACATGGAGGCGGCCGCCGCGGGATGGCCAGGCGCGGCATTGCTGCGGGTGGATTCCCGCAATCGCGTGCTGGTCGCCAACGGCCGGGTGTTGCTTGGCGCGGCCATCGAGCTGGCCGACAAGCCACCGCCAGAGGCGGTATTCCTGGGTCGCGTCGAGGGCGGCCGCCACGTCTGGGCGGTGCGGGCAGCGCTGCAGCCGATCGCTGATCCCGACATACCAGCCGAGGCGGTGGACCTTCGTGGGCTCGGCCGAATCATGGACGACACCAGCAGCCAACTGGTGTCGTCGGCATCGGCGCTGTTGAACTGGCATGACAACGCACGATTCAGCGCCCTAGACGGCGCGCCGACGAAACCGGCCAGGGCCGGCTGGTCACGGGTCAACCCGATCACCGGTCATGAGGAGTTCCCCCGTATCGACCCGGCGGTGATCTGCCTGGTTCACGACGGCGCTGATCGTGCCGTGTTGGCTCGCCAGGCGGCGTGGCCGGAACGGATGTTCTCGCTGTTGGCTGGCTTTGTCGAGGCCGGAGAGTCGTTCGAAGTCTGCGTCGCCCGGGAGATCCGCGAGGAAATCGGCCTGACCGTTCGCGATGTGCGCTATCTGGGCAGCCAGCAGTGGCCGTTCCCGCGGTCGTTAATGGTTGGCTTTCATGCCTTGGGTGACCCGGATGAGGAGTTCTCGTTCAGCGACGGCGAAATCGCCGAAGCCGCGTGGTTCACCCGCGATGAGGTGCGCGCAGCGCTTGCCGCCGGCGATTGGTCCAGTGCGTCGGAGTCGAAACTGCTACTGCCCGGGTCGATCTCGATCGCCCGCGTGATCATCGAATCGTGGGCAGCGTGCGAATGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004931", "ARO_id": "43117", "ARO_name": "Mycobacterium tuberculosis nudC mutations conferring resistance to isoniazid", "CARD_short_name": "Mtub_nudC_INH", "ARO_description": "Mutations that occur in nudC which through overexpression of the enzyme can result in or contribute to antibiotic resistance to isoniazid.", "ARO_category": {"43097": {"category_aro_accession": "3004911", "category_aro_cvterm_id": "43097", "category_aro_name": "isoniazid resistant nudC", "category_aro_description": "nudC is a NADH pyrophosphatase that is involved in nicotinate and nicotinamide metabolism. Mutations that occur on the nudC gene resulting in the inability for isoniazid to function.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3706": {"model_id": "3706", "model_name": "Mycobacterium tuberculosis ponA1 mutations confer resistance to rifabutin", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"41344": {"param_type": "insertion mutation from peptide sequence", "param_description": "A subtype of the insertion mutation detection model parameter is used when a set of insertion mutations are reported in a peptide sequence format, encoded as [+][AAs][position range], for example +D345 or +MPL110-112.", "param_type_id": "41344", "param_value": {"9738": "P627_P629dup", "9758": "V624_P626dup", "9759": "P627dup", "9765": "+PPW631", "9760": "P626_P628dup"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9739": "G363D", "9740": "Q365H", "9749": "T658A", "9753": "I41M", "9755": "A516T"}, "clinical": {"9739": "G363D", "9740": "Q365H", "9749": "T658A", "9753": "I41M", "9755": "A516T"}}, "41342": {"param_type": "deletion mutation from peptide sequence", "param_description": "A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a peptide sequence format, encoded as [-][AAs][position range], for example -K527 or -QN517-518.", "param_type_id": "41342", "param_value": {"9762": "-P631"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "1275"}}, "model_sequences": {"sequence": {"8789": {"protein_sequence": {"accession": "YP_177687.1", "sequence": "MVILLPMVTFTMAYLIVDVPKPGDIRTNQVSTILASDGSEIAKIVPPEGNRVDVNLSQVPMHVRQAVIAAEDRNFYSNPGFSFTGFARAVKNNLFGGDLQGGSTITQQYVKNALVGSAQHGWSGLMRKAKELVIATKMSGEWSKDDVLQAYLNIIYFGRGAYGISAASKAYFDKPVEQLTVAEGALLAALIRRPSTLDPAVDPEGAHARWNWVLDGMVETKALSPNDRAAQVFPETVPPDLARAENQTKGPNGLIERQVTRELLELFNIDEQTLNTQGLVVTTTIDPQAQRAAEKAVAKYLDGQDPDMRAAVVSIDPHNGAVRAYYGGDNANGFDFAQAGLQTGSSFKVFALVAALEQGIGLGYQVDSSPLTVDGIKITNVEGEGCGTCNIAEALKMSLNTSYYRLMLKLNGGPQAVADAAHQAGIASSFPGVAHTLSEDGKGGPPNNGIVLGQYQTRVIDMASAYATLAASGIYHPPHFVQKVVSANGQVLFDASTADNTGDQRIPKAVADNVTAAMEPIAGYSRGHNLAGGRDSAAKTGTTQFGDTTANKDAWMVGYTPSLSTAVWVGTVKGDEPLVTASGAAIYGSGLPSDIWKATMDGALKGTSNETFPKPTEVGGYAGVPPPPPPPEVPPSETVIQPTVEIAPGITIPIGPPTTITLAPPPPAPPAATPTPPP"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "53662", "fmax": "55699", "strand": "+", "sequence": "GTGGTGATCCTGTTGCCGATGGTCACCTTCACGATGGCCTACCTGATCGTCGACGTTCCCAAGCCAGGTGACATCCGTACCAACCAGGTCTCCACGATCCTTGCCAGCGACGGCTCGGAAATCGCCAAAATTGTTCCGCCCGAAGGTAATCGGGTCGACGTCAACCTCAGCCAGGTGCCGATGCATGTGCGCCAGGCGGTGATTGCGGCCGAAGACCGCAATTTCTATTCGAATCCGGGATTCTCGTTCACCGGCTTCGCGCGGGCAGTCAAGAACAACCTGTTCGGCGGCGATCTGCAGGGCGGATCGACGATTACCCAGCAGTACGTCAAGAACGCGCTGGTCGGTTCCGCACAGCACGGGTGGAGCGGTCTGATGCGCAAGGCGAAAGAATTGGTCATCGCGACGAAGATGTCGGGGGAGTGGTCTAAAGACGATGTGCTGCAGGCGTATCTGAACATCATCTACTTCGGCCGGGGCGCCTACGGCATTTCGGCGGCGTCCAAGGCTTATTTCGACAAGCCCGTCGAGCAGCTGACCGTTGCCGAAGGGGCGTTGTTGGCAGCGCTGATTCGGCGGCCTTCGACGCTGGACCCGGCGGTCGACCCCGAAGGGGCCCATGCCCGCTGGAATTGGGTACTCGACGGCATGGTGGAAACCAAGGCTCTCTCGCCGAATGACCGTGCGGCGCAGGTGTTTCCCGAGACAGTGCCGCCCGATCTGGCCCGGGCAGAGAATCAGACCAAAGGACCCAACGGGCTGATCGAGCGGCAGGTGACAAGGGAGTTGCTCGAGCTGTTCAACATCGACGAGCAGACCCTCAACACCCAGGGGCTGGTGGTCACCACCACGATTGATCCGCAGGCCCAACGGGCGGCGGAGAAGGCGGTTGCGAAATACCTGGACGGGCAGGACCCCGACATGCGTGCCGCCGTGGTTTCCATCGACCCGCACAACGGGGCGGTGCGTGCGTACTACGGTGGCGACAATGCCAATGGCTTTGACTTCGCTCAAGCGGGATTGCAGACTGGATCGTCGTTTAAGGTGTTTGCTCTGGTGGCCGCCCTTGAGCAGGGGATCGGCCTGGGCTACCAGGTAGACAGCTCTCCGTTGACGGTCGACGGCATCAAGATCACCAACGTCGAGGGCGAGGGTTGCGGGACGTGCAACATCGCCGAGGCGCTCAAAATGTCGCTGAACACCTCCTACTACCGGCTGATGCTCAAGCTCAACGGCGGCCCACAGGCTGTGGCCGATGCCGCGCACCAAGCCGGCATTGCCTCCAGCTTCCCGGGCGTTGCGCACACGCTGTCCGAAGATGGCAAGGGTGGACCGCCCAACAACGGGATCGTGTTGGGCCAGTACCAAACCCGGGTGATCGACATGGCATCGGCGTATGCCACGTTGGCCGCGTCCGGTATCTACCACCCGCCGCATTTCGTACAGAAGGTGGTCAGTGCCAACGGCCAGGTCCTCTTCGACGCCAGCACCGCGGACAACACCGGCGATCAGCGCATCCCCAAGGCGGTAGCCGACAACGTGACTGCGGCGATGGAGCCGATCGCAGGTTATTCGCGTGGCCACAACCTAGCGGGTGGGCGGGATTCGGCGGCCAAGACCGGCACTACGCAATTTGGTGACACCACCGCGAACAAAGACGCCTGGATGGTCGGGTACACGCCGTCGTTGTCTACGGCTGTGTGGGTGGGCACCGTCAAGGGTGACGAGCCACTGGTAACCGCTTCGGGTGCAGCGATTTACGGCTCGGGCCTGCCGTCGGACATCTGGAAGGCAACCATGGACGGCGCCTTGAAGGGCACGTCGAACGAGACTTTCCCCAAACCGACCGAGGTCGGTGGTTATGCCGGTGTGCCGCCGCCGCCGCCGCCGCCGGAGGTACCACCTTCGGAGACCGTCATCCAGCCCACGGTCGAAATTGCGCCGGGGATTACCATCCCGATCGGTCCCCCGACCACCATTACCCTGGCGCCACCGCCCCCGGCCCCGCCCGCTGCGACTCCCACGCCGCCGCCGTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004960", "ARO_id": "43146", "ARO_name": "Mycobacterium tuberculosis ponA1 mutations confer resistance to rifabutin", "CARD_short_name": "Mtub_ponA1_RFB", "ARO_description": "Mutations in ponA1 that contribute to or confer resistance to rifabutin antibiotic.", "ARO_category": {"43145": {"category_aro_accession": "3004959", "category_aro_cvterm_id": "43145", "category_aro_name": "rifamycin resistant ponA1", "category_aro_description": "Mutations in the ponA1 gene that can contribute to or confer resistance to rifamycin-class antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "36308": {"category_aro_accession": "3000169", "category_aro_cvterm_id": "36308", "category_aro_name": "rifampin", "category_aro_description": "Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.", "category_aro_class_name": "Antibiotic"}, "36669": {"category_aro_accession": "3000530", "category_aro_cvterm_id": "36669", "category_aro_name": "rifabutin", "category_aro_description": "Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.", "category_aro_class_name": "Antibiotic"}, "36296": {"category_aro_accession": "3000157", "category_aro_cvterm_id": "36296", "category_aro_name": "rifamycin antibiotic", "category_aro_description": "Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3735": {"model_id": "3735", "model_name": "Mycobacterium tuberculosis sigI mutations conferring resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9592": "K270Q"}, "clinical": {"9592": "K270Q"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"8785": {"protein_sequence": {"accession": "NP_215249.1", "sequence": "MARVSGAAAAEAALMRALYDEHAAVLWRYALRLTGDAAQAEDVVQETLLRAWQHPEVIGDTARPARAWLFTVARNMIIDERRSARFRNVVGSTDQSGTPEQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVTR"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "827542", "fmax": "828076", "strand": "+", "sequence": "GTGGCTCGTGTGTCGGGCGCCGCGGCCGCTGAAGCCGCGTTGATGAGGGCGCTCTACGACGAGCATGCCGCCGTGTTGTGGCGTTACGCGCTGCGCTTGACCGGGGATGCGGCCCAAGCCGAAGACGTCGTCCAAGAGACGCTGTTGCGGGCGTGGCAGCATCCGGAGGTGATCGGCGACACCGCGCGGCCGGCAAGGGCGTGGTTGTTCACCGTCGCGCGCAACATGATCATCGACGAGCGGCGCAGCGCCCGGTTCCGCAATGTGGTCGGTTCGACCGACCAATCGGGCACACCCGAGCAGTCGACGCCGGACGAGGTGAACGCCGCACTGGATCGGCTGCTGATCGCCGATGCGCTGGCCCAACTGTCCGCCGAGCATAGGGCCGTGATCCAGCGGTCCTACTACCGCGGATGGTCGACCGCACAGATTGCCACCGACCTCGGAATTGCCGAAGGAACGGTGAAGTCGCGATTGCACTACGCCGTGCGCGCGTTGCGGCTCACTCTGCAGGAACTGGGAGTTACTCGATGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004932", "ARO_id": "43118", "ARO_name": "Mycobacterium tuberculosis sigI mutations conferring resistance to isoniazid", "CARD_short_name": "Mtub_sigI_INH", "ARO_description": "Mycobacterium tuberculosis sigI mutations conferring resistance to isoniazid.", "ARO_category": {"43099": {"category_aro_accession": "3004913", "category_aro_cvterm_id": "43099", "category_aro_name": "isoniazid resistant sigI", "category_aro_description": "A sigma factor that acts as an initiation factor that promotes attachment of the RNA polymerase to specific initiation sites and then is released. Transcriptional analyses indicate that katG is also regulated by the sigma factor sigl and indicate resistance to isoniaizd.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3709": {"model_id": "3709", "model_name": "Mycobacterium tuberculosis whib7 mutation conferring resistance to streptomycin", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"41339": {"param_type": "snp in promoter region", "param_description": "A SNP in the promoter region of a gene which alters transcription of that gene, encoded as [wild-type][-][position][mutation], for example t-11c. Var represents any possible substitution. This is a pilot parameter in need of further documentation.", "param_type_id": "41339", "param_value": {"13186": "a-116g"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"13014": "T57G"}, "clinical": {"13014": "T57G"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "125"}}, "model_sequences": {"sequence": {"8798": {"protein_sequence": {"accession": "YP_177940.1", "sequence": "MSVLTVPRQTPRQRLPVLPCHVGDPDLWFADTPAGLEVAKTLCVSCPIRRQCLAAALQRAEPWGVWGGEIFDQGSIVSHKRPRGRPRKDAVA"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3568400", "fmax": "3568679", "strand": "-", "sequence": "GTGTCGGTACTGACAGTCCCCAGACAGACCCCCAGACAAAGATTGCCGGTTTTGCCGTGCCACGTCGGTGATCCCGATCTGTGGTTCGCCGATACCCCGGCCGGTCTCGAGGTAGCCAAGACACTGTGTGTGAGCTGCCCGATCAGGCGGCAGTGCTTGGCCGCGGCGCTTCAGCGGGCTGAACCCTGGGGCGTTTGGGGTGGTGAGATATTCGACCAAGGCTCGATCGTGAGTCACAAGCGTCCGCGCGGACGTCCGCGCAAGGATGCTGTTGCATAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004968", "ARO_id": "43154", "ARO_name": "Mycobacterium tuberculosis whib7 mutation conferring resistance to streptomycin", "CARD_short_name": "Mtub_whib7_STR", "ARO_description": "Mutations in whib7 that can contribute to or confer resistance to streptomycin.", "ARO_category": {"43151": {"category_aro_accession": "3004965", "category_aro_cvterm_id": "43151", "category_aro_name": "streptomycin resistant whib7", "category_aro_description": "A protein involved in transcriptional mechanisms. Mutations in the gene can cause resistance to streptomycin.", "category_aro_class_name": "AMR Gene Family"}, "35958": {"category_aro_accession": "0000040", "category_aro_cvterm_id": "35958", "category_aro_name": "streptomycin", "category_aro_description": "Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.", "category_aro_class_name": "Antibiotic"}, "35935": {"category_aro_accession": "0000016", "category_aro_cvterm_id": "35935", "category_aro_name": "aminoglycoside antibiotic", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3742": {"model_id": "3742", "model_name": "Mycobacterium tuberculosis ddlA mutations confer resistance to cycloserine", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "675"}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"13184": "T365A"}, "clinical": {"13184": "T365A"}}}, "model_sequences": {"sequence": {"8824": {"protein_sequence": {"accession": "NP_217497.1", "sequence": "MSANDRRDRRVRVAVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNRELPQVKSGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLARGVGLH"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3336795", "fmax": "3337917", "strand": "-", "sequence": "GTGAGTGCTAACGACCGGCGTGATCGGCGTGTCCGCGTTGCCGTCGTGTTCGGCGGGCGCAGCAACGAGCACGCCATCTCGTGTGTGTCCGCCGGCAGCATCCTGCGCAACCTGGACTCGCGGCGGTTCGACGTGATCGCGGTGGGTATCACCCCGGCAGGTTCGTGGGTGCTCACCGACGCCAACCCCGACGCCCTGACGATCACCAACCGGGAGCTTCCTCAGGTCAAATCAGGATCGGGCACCGAGCTGGCGCTGCCGGCCGATCCGCGGCGTGGTGGCCAGTTGGTGTCGCTGCCGCCCGGGGCCGGCGAGGTTCTGGAGTCGGTCGACGTGGTGTTCCCGGTACTGCACGGCCCGTACGGCGAGGACGGCACGATCCAGGGACTGCTCGAACTCGCCGGGGTGCCCTACGTGGGCGCCGGTGTGCTGGCCAGTGCCGTCGGCATGGACAAGGAGTTCACCAAGAAGCTGCTCGCCGCCGATGGACTTCCGGTGGGTGCGTACGCGGTGCTGCGTCCGCCGCGGTCGACACTGCACCGCCAGGAGTGCGAACGGCTGGGCTTACCGGTGTTCGTCAAACCCGCCCGAGGCGGCTCGTCGATCGGTGTTAGCCGGGTGTCGAGTTGGGATCAACTGCCCGCCGCGGTCGCGCGGGCCCGCCGGCATGACCCTAAGGTCATCGTCGAGGCCGCGATCAGCGGCCGCGAGCTGGAATGCGGTGTGCTCGAAATGCCGGACGGCACACTGGAAGCCAGCACGCTGGGGGAGATCCGGGTGGCCGGGGTGCGGGGACGCGAGGACTCTTTCTACGACTTCGCAACCAAGTATCTCGACGACGCAGCCGAATTGGACGTGCCCGCCAAGGTCGATGACCAGGTCGCAGAGGCGATTCGTCAGCTGGCGATCCGGGCGTTCGCGGCTATCGACTGCCGGGGTCTGGCCAGGGTGGACTTCTTCCTCACCGACGACGGTCCGGTGATCAACGAGATCAACACGATGCCGGGATTCACCACGATCTCGATGTACCCGCGGATGTGGGCGGCCAGCGGTGTCGACTATCCGACCCTGCTGGCGACGATGATCGAGACGACATTGGCCCGCGGCGTGGGCCTGCACTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004941", "ARO_id": "43127", "ARO_name": "Mycobacterium tuberculosis ddlA mutations confer resistance to cycloserine", "CARD_short_name": "Mtub_ddlA_DCS", "ARO_description": "Point mutations that occur within Mycobacterium tuberculosis ddlA gene resulting in resistance to cycloserine.", "ARO_category": {"43125": {"category_aro_accession": "3004939", "category_aro_cvterm_id": "43125", "category_aro_name": "cycloserine resistant ddlA", "category_aro_description": "ddlA catalyzes the ATP-driven ligation of two D-alanine molecules to form the D-alanyl-D-alanine dipeptide, key in forming the cell wall. Cycloserine has a similar structure to d-alanine and inhibits the growth of the cell wall.", "category_aro_class_name": "AMR Gene Family"}, "37140": {"category_aro_accession": "3000760", "category_aro_cvterm_id": "37140", "category_aro_name": "cycloserine", "category_aro_description": "Cycloserine is an anti-mycobacterial agent, and is active against enterobacteria, streptococci, M. tuberculosis, Staphylococcus aureus, and many Gram-negative and Gram-positive bacteria. It inhibits cell wall biosynthesis.", "category_aro_class_name": "Antibiotic"}, "45736": {"category_aro_accession": "3007154", "category_aro_cvterm_id": "45736", "category_aro_name": "cycloserine-like antibiotic", "category_aro_description": "A group of antibiotics including cycloserine and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3746": {"model_id": "3746", "model_name": "Mycobacterium tuberculosis rpoC mutations confer resistance to rifampicin", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9744": "V483G", "9800": "N416S", "9801": "V431M", "9802": "G433S", "9803": "P434L", "9804": "K445R", "9805": "F452S", "9806": "V483A", "9808": "W484G", "9809": "D485Y", "9810": "I491V", "9811": "I491T", "9812": "L507V", "9813": "L516P", "9815": "Q523E", "9816": "H525Q", "9817": "L527V", "9820": "Y61Y", "9823": "N698S", "9824": "A734V", "9825": "E750Q", "9827": "P1040A", "9828": "P1040S", "9829": "P1040R", "9830": "P1040L", "9831": "E1092D", "9832": "Q1110H", "9833": "E1113G", "9834": "Q1125H", "9835": "T1230I", "9837": "V1252L", "9839": "G332S", "9814": "V517L", "9836": "V1252M"}, "clinical": {"9744": "V483G", "9800": "N416S", "9801": "V431M", "9802": "G433S", "9803": "P434L", "9804": "K445R", "9805": "F452S", "9806": "V483A", "9808": "W484G", "9809": "D485Y", "9810": "I491V", "9811": "I491T", "9812": "L507V", "9813": "L516P", "9815": "Q523E", "9816": "H525Q", "9817": "L527V", "9820": "Y61Y", "9823": "N698S", "9824": "A734V", "9825": "E750Q", "9827": "P1040A", "9828": "P1040S", "9829": "P1040R", "9830": "P1040L", "9831": "E1092D", "9832": "Q1110H", "9833": "E1113G", "9834": "Q1125H", "9835": "T1230I", "9837": "V1252L", "9839": "G332S", "9814": "V517L", "9836": "V1252M"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "1100"}}, "model_sequences": {"sequence": {"8801": {"protein_sequence": {"accession": "NP_215182.1", "sequence": "MLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAYTIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYR"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "763369", "fmax": "767320", "strand": "+", "sequence": "GTGCTCGACGTCAACTTCTTCGATGAACTCCGCATCGGTCTTGCTACCGCGGAGGACATCAGGCAATGGTCCTATGGCGAGGTCAAAAAGCCGGAGACGATCAACTACCGCACGCTTAAGCCGGAGAAGGACGGCCTGTTCTGCGAGAAGATCTTCGGGCCGACTCGCGACTGGGAATGCTACTGCGGCAAGTACAAGCGGGTGCGCTTCAAGGGCATCATCTGCGAGCGCTGCGGCGTCGAGGTGACCCGCGCCAAGGTGCGTCGTGAGCGGATGGGCCACATCGAGCTTGCCGCGCCCGTCACCCACATCTGGTACTTCAAGGGTGTGCCCTCGCGGCTGGGGTATCTGCTGGACCTGGCCCCGAAGGACCTGGAGAAGATCATCTACTTCGCTGCCTACGTGATCACCTCGGTCGACGAGGAGATGCGCCACAATGAGCTCTCCACGCTCGAGGCCGAAATGGCGGTGGAGCGCAAGGCCGTCGAAGACCAGCGCGACGGCGAACTAGAGGCCCGGGCGCAAAAGCTGGAGGCCGACCTGGCCGAGCTGGAGGCCGAGGGCGCCAAGGCCGATGCGCGGCGCAAGGTTCGCGACGGCGGCGAGCGCGAGATGCGCCAGATCCGTGACCGCGCGCAGCGTGAGCTGGACCGGTTGGAGGACATCTGGAGCACTTTCACCAAGCTGGCGCCCAAGCAGCTGATCGTCGACGAAAACCTCTACCGCGAACTCGTCGACCGCTACGGCGAGTACTTCACCGGTGCCATGGGCGCGGAGTCGATCCAGAAGCTGATCGAGAACTTCGACATCGACGCCGAAGCCGAGTCGCTGCGGGATGTCATCCGAAACGGCAAGGGGCAGAAGAAGCTTCGCGCCCTCAAGCGGCTGAAGGTGGTTGCGGCGTTCCAACAGTCGGGCAACTCGCCGATGGGCATGGTGCTCGACGCCGTCCCGGTGATCCCGCCGGAGCTGCGCCCGATGGTGCAGCTCGACGGCGGCCGGTTCGCCACGTCCGACTTGAACGACCTGTACCGCAGGGTGATCAACCGCAACAACCGGCTGAAAAGGCTGATCGATCTGGGTGCGCCGGAAATCATCGTCAACAACGAGAAGCGGATGCTGCAGGAATCCGTGGACGCGCTGTTCGACAATGGCCGCCGCGGCCGGCCCGTCACCGGGCCGGGCAACCGTCCGCTCAAGTCGCTTTCCGATCTGCTCAAGGGCAAGCAGGGCCGGTTCCGGCAGAACCTGCTCGGCAAGCGTGTCGACTACTCGGGCCGGTCGGTCATCGTGGTCGGCCCGCAGCTCAAGCTGCACCAGTGCGGTCTGCCCAAGCTGATGGCGCTGGAGCTGTTCAAGCCGTTCGTGATGAAGCGGCTGGTGGACCTCAACCATGCGCAGAACATCAAGAGCGCCAAGCGCATGGTGGAGCGCCAGCGCCCCCAAGTGTGGGATGTGCTCGAAGAGGTCATCGCCGAGCACCCGGTGTTGCTGAACCGCGCACCCACCCTGCACCGGTTGGGTATCCAGGCCTTCGAGCCAATGCTGGTGGAAGGCAAGGCCATTCAGCTGCACCCGTTGGTGTGTGAGGCGTTCAATGCCGACTTCGACGGTGACCAGATGGCCGTGCACCTGCCTTTGAGCGCCGAAGCGCAGGCCGAGGCTCGCATTTTGATGTTGTCCTCCAACAACATCCTGTCGCCGGCATCTGGGCGTCCGTTGGCCATGCCGCGGCTGGACATGGTGACCGGGCTGTACTACCTGACCACCGAGGTCCCCGGGGACACCGGCGAATACCAGCCGGCCAGCGGGGATCACCCGGAGACTGGTGTCTACTCTTCGCCGGCCGAAGCGATCATGGCGGCCGACCGCGGTGTCTTGAGCGTGCGGGCCAAGATCAAGGTGCGGCTGACCCAGCTGCGGCCGCCGGTCGAGATCGAGGCCGAGCTATTCGGCCACAGCGGCTGGCAGCCGGGCGATGCGTGGATGGCCGAGACCACGCTGGGCCGGGTGATGTTCAACGAGCTGCTGCCGCTGGGTTATCCGTTCGTCAACAAGCAGATGCACAAGAAGGTGCAGGCCGCCATCATCAACGACCTGGCCGAGCGTTACCCGATGATCGTGGTCGCCCAGACCGTCGACAAGCTCAAGGACGCCGGCTTCTACTGGGCCACCCGCAGCGGCGTGACGGTGTCGATGGCCGACGTGCTGGTGCCGCCGCGCAAGAAGGAGATCCTCGACCACTACGAGGAGCGCGCGGACAAGGTCGAAAAGCAGTTCCAGCGTGGCGCTTTGAACCACGACGAGCGCAACGAGGCGCTGGTGGAGATTTGGAAGGAAGCCACCGACGAGGTCGGTCAGGCGTTGCGGGAGCACTACCCCGACGACAACCCGATCATCACCATCGTCGACTCCGGCGCCACCGGCAACTTCACCCAGACTCGAACGCTGGCCGGTATGAAGGGCCTGGTGACCAACCCGAAGGGTGAGTTCATCCCGCGTCCGGTCAAGTCCTCCTTCCGTGAGGGCCTGACCGTGCTGGAGTACTTCATCAACACCCACGGCGCTCGAAAGGGCTTGGCGGACACCGCGTTGCGCACCGCCGACTCCGGCTACCTGACCCGACGTCTGGTGGACGTGTCCCAGGACGTGATCGTGCGCGAGCACGACTGCCAGACCGAGCGCGGCATCGTCGTCGAGCTGGCCGAGCGTGCACCCGACGGCACGCTGATCCGCGACCCGTACATCGAAACCTCGGCCTACGCGCGGACCCTGGGCACCGACGCGGTCGACGAGGCCGGCAACGTCATCGTCGAGCGTGGTCAAGACCTGGGCGATCCGGAGATTGACGCTCTGTTGGCTGCTGGTATTACCCAGGTCAAGGTGCGTTCGGTGCTGACGTGTGCCACCAGCACCGGCGTGTGCGCGACCTGCTACGGGCGTTCCATGGCCACCGGCAAGCTGGTCGACATCGGTGAAGCCGTCGGCATCGTGGCCGCCCAGTCCATCGGCGAACCCGGCACCCAGCTGACCATGCGCACCTTCCACCAGGGTGGCGTCGGTGAGGACATCACCGGTGGTCTGCCCCGGGTGCAGGAGCTGTTCGAGGCCCGGGTACCGCGTGGCAAGGCGCCGATCGCCGACGTCACCGGCCGGGTTCGGCTCGAGGACGGCGAGCGGTTCTACAAGATCACCATCGTTCCTGACGACGGCGGTGAGGAAGTGGTCTACGACAAGATCTCCAAGCGGCAGCGGCTGCGGGTGTTCAAGCACGAAGACGGTTCCGAACGGGTGCTCTCCGATGGCGACCACGTCGAGGTGGGCCAGCAGCTGATGGAAGGCTCGGCCGACCCGCATGAGGTGCTGCGGGTGCAGGGCCCCCGCGAGGTGCAGATACACCTGGTTCGCGAGGTCCAGGAGGTCTACCGCGCCCAAGGTGTGTCGATCCACGACAAGCACATCGAGGTGATCGTTCGCCAGATGCTGCGCCGGGTGACCATCATCGACTCGGGCTCGACGGAGTTTTTGCCTGGCTCGCTGATCGACCGCGCGGAGTTCGAGGCAGAGAACCGCCGAGTGGTGGCCGAGGGCGGTGAGCCCGCGGCCGGCCGTCCGGTGCTGATGGGCATCACGAAGGCGTCGCTGGCCACCGACTCGTGGCTGTCGGCGGCGTCGTTCCAGGAGACCACTCGCGTGCTGACCGATGCGGCGATCAACTGCCGCAGCGATAAGCTCAACGGTCTGAAGGAAAACGTGATCATCGGCAAGCTGATCCCGGCCGGTACCGGTATCAACCGCTACCGCAACATCGCGGTGCAGCCCACCGAGGAGGCCCGCGCTGCGGCGTACACCATCCCGTCGTATGAGGATCAGTACTACAGCCCGGACTTCGGTGCGGCCACCGGTGCTGCCGTCCCGCTGGACGACTACGGCTACAGCGACTACCGCTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004994", "ARO_id": "43181", "ARO_name": "Mycobacterium tuberculosis rpoC mutations confer resistance to rifampicin", "CARD_short_name": "Mtub_rpoC_RIF", "ARO_description": "Mutations in rpoC that contribute to or confer resistance to rifampicin antibiotic.", "ARO_category": {"43182": {"category_aro_accession": "3004995", "category_aro_cvterm_id": "43182", "category_aro_name": "rifampicin resistant rpoC", "category_aro_description": "rpoC catalyzes the transcription of DNA into RNA and mutations confer resistance to rifampicin.", "category_aro_class_name": "AMR Gene Family"}, "36308": {"category_aro_accession": "3000169", "category_aro_cvterm_id": "36308", "category_aro_name": "rifampin", "category_aro_description": "Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.", "category_aro_class_name": "Antibiotic"}, "36669": {"category_aro_accession": "3000530", "category_aro_cvterm_id": "36669", "category_aro_name": "rifabutin", "category_aro_description": "Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.", "category_aro_class_name": "Antibiotic"}, "36296": {"category_aro_accession": "3000157", "category_aro_cvterm_id": "36296", "category_aro_name": "rifamycin antibiotic", "category_aro_description": "Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3747": {"model_id": "3747", "model_name": "Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9769": "V183A", "9770": "V183G", "9771": "T187A", "9773": "G31S"}, "clinical": {"9769": "V183A", "9770": "V183G", "9771": "T187A", "9773": "G31S"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "600"}}, "model_sequences": {"sequence": {"8797": {"protein_sequence": {"accession": "NP_217974.1", "sequence": "MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEVAGYDVATGTWSTEGAYDEQDYAETEQL"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3877463", "fmax": "3878507", "strand": "-", "sequence": "ATGCTGATCTCACAGCGCCCCACCCTGTCCGAGGACGTCCTCACCGACAACCGATCCCAGTTCGTGATCGAACCGCTGGAGCCGGGATTCGGCTACACCCTGGGCAATTCGCTGCGTCGCACCCTGCTGTCGTCGATTCCCGGAGCGGCCGTCACCAGCATTCGCATCGATGGTGTACTGCACGAATTCACCACGGTGCCCGGGGTCAAAGAAGATGTCACCGAGATCATCCTGAATCTCAAGAGCCTGGTGGTGTCCTCGGAGGAGGACGAGCCGGTCACCATGTACCTACGCAAGCAGGGTCCGGGTGAGGTTACCGCCGGCGACATCGTGCCGCCGGCCGGCGTCACCGTGCACAACCCCGGCATGCACATCGCCACGCTGAACGATAAGGGCAAGCTGGAAGTCGAGCTCGTCGTCGAGCGTGGCCGCGGCTATGTCCCGGCGGTGCAAAACCGGGCTTCGGGTGCCGAAATTGGGCGCATTCCAGTCGATTCCATCTACTCACCGGTGCTCAAAGTGACCTACAAGGTGGACGCCACCCGGGTCGAGCAGCGCACCGACTTCGACAAGCTGATCCTGGACGTGGAGACCAAGAATTCAATCAGCCCGCGCGACGCGCTGGCGTCGGCTGGCAAGACGCTGGTCGAGTTGTTCGGCCTGGCACGGGAACTCAACGTCGAGGCCGAAGGCATCGAGATCGGGCCGTCGCCGGCCGAGGCCGATCACATTGCGTCATTCGCCCTGCCGATCGACGACCTGGATCTGACGGTGCGGTCCTACAACTGCCTCAAGCGCGAGGGGGTGCACACCGTGGGCGAACTGGTGGCGCGCACCGAATCCGACCTGCTTGACATCCGCAACTTCGGTCAGAAGTCCATCGACGAGGTGAAGATCAAGCTGCACCAGCTGGGCCTGTCACTCAAGGACAGCCCGCCGAGCTTCGACCCCTCGGAGGTCGCGGGCTACGACGTCGCCACCGGCACCTGGTCGACCGAGGGCGCGTACGACGAGCAGGACTACGCCGAAACCGAACAGCTTTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004999", "ARO_id": "43186", "ARO_name": "Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin", "CARD_short_name": "Mtub_rpoA_RIF", "ARO_description": "Mutations in rpoA that contribute to or confer resistance to rifampicin antibiotic.", "ARO_category": {"43185": {"category_aro_accession": "3004998", "category_aro_cvterm_id": "43185", "category_aro_name": "rifampicin resistant rpoA", "category_aro_description": "rpoA catalyzes the transcription of DNA into RNA and mutations confer resistance to rifampicin.", "category_aro_class_name": "AMR Gene Family"}, "36308": {"category_aro_accession": "3000169", "category_aro_cvterm_id": "36308", "category_aro_name": "rifampin", "category_aro_description": "Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.", "category_aro_class_name": "Antibiotic"}, "36296": {"category_aro_accession": "3000157", "category_aro_cvterm_id": "36296", "category_aro_name": "rifamycin antibiotic", "category_aro_description": "Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3712": {"model_id": "3712", "model_name": "Mycobacterium tuberculosis ppsC mutations confer resistance to pyrazinamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9707": "A957P", "9708": "N1899S"}, "clinical": {"9707": "A957P", "9708": "N1899S"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "4250"}}, "model_sequences": {"sequence": {"8791": {"protein_sequence": {"accession": "NP_217449.1", "sequence": "MTAATPDRRAIITEALHKIDDLTARLEIAEKSSSEPIAVIGMGCRFPGGVNNPEQFWDLLCAGRSGIVRVPAQRWDADAYYCDDHTVPGTICSTEGGFLTSWQPDEFDAEFFSISPREAAAMDPQQRLLIEVAWEALEDAGVPQHTIRGTQTSVFVGVTAYDYMLTLAGRLRPVDLDAYIPTGNSANFAAGRLAYILGARGPAVVIDTACSSSLVAVHLACQSLRGRESDMALVGGTNLLLSPGPSIACSRWGMLSPEGRCKTFDASADGYVRGEGAAVVVLKRLDDAVRDGNRILAVVRGSAVNQDGASSGVTVPNGPAQQALLAKALTSSKLTAADIDYVEAHGTGTPLGDPIELDSLSKVFSDRAGSDQLVIGSVKTNLGHLEAAAGVAGLMKAVLAVHNGYIPRHLNFHQLTPHASEAASRLRIAADGIDWPTTGRPRRAGVSSFGVSGTNAHVVIEQAPDPMAAAGTEPQRGPVPAVSTLVVFGKTAPRVAATASVLADWLDGPGAAVPLADVAHTLNHHRARQTRFGTVAAVDRRQAVIGLRALAAGQSAPGVVAPREGSIGGGTVFVYSGRGSQWAGMGRQLLADEPAFAAAIAELEPEFVAQGGFSLRDVIAGGKELVGIEQIQLGLIGMQLALTALWRSYGVTPDAVIGHSMGEVAAAVVAGALTPAQGLRVTAVRSRLMAPLSGQGTMALLELDAEATEALIADYPEVSLGIYASPRQTVISGPPLLIDELIDKVRQQNGFATRVNIEVAPHNPAMDALQPAMRSELADLTPQPPTIPIISTTYADLGISLGSGPRFDAEHWATNMRNPVRFHQAIAHAGADHHTFIEISAHPLLTHSISDTLRASYDVDNYLSIGTLQRDAHDTLEFHTNLNTTHTTHPPQTPHPPEPHPVLPTTPWQHTQHWITATSAAYHRPDTHPLLGVGVTDPTNGTRVWESELDPDLLWLADHVIDDLVVLPGAAYAEIALAAATDTFAVEQDQPWMISELDLRQMLHVTPGTVLVTTLTGDEQRCQVEIRTRSGSSGWTTHATATVARAEPLAPLDHEGQRREVTTADLEDQLDPDDLYQRLRGAGQQHGPAFQGIVGLAVTQAGVARAQVRLPASARTGSREFMLHPVMMDIALQTLGATRTATDLAGGQDARQGPSSNSALVVPVRFAGVHVYGDITRGVRAVGSLAAAGDRLVGEVVLTDANGQPLLVVDEVEMAVLGSGSGATELTNRLFMLEWEPAPLEKTAEATGALLLIGDPAAGDPLLPALQSSLRDRITDLELASAADEATLRAAISRTSWDGIVVVCPPRANDESMPDEAQLELARTRTLLVASVVETVTRMGARKSPRLWIVTRGAAQFDAGESVTLAQTGLRGIARVLTFEHSELNTTLVDIEPDGTGSLAALAEELLAGSEADEVALRDGQRYVNRLVPAPTTTSGDLAAEARHQVVNLDSSGASRAAVRLQIDQPGRLDALNVHEVKRGRPQGDQVEVRVVAAGLNFSDVLKAMGVYPGLDGAAPVIGGECVGYVTAIGDEVDGVEVGQRVIAFGPGTFGTHLGTIADLVVPIPDTLADNEAATFGVAYLTAWHSLCEVGRLSPGERVLIHSATGGVGMAAVSIAKMIGARIYTTAGSDAKREMLSRLGVEYVGDSRSVDFADEILELTDGYGVDVVLNSLAGEAIQRGVQILAPGGRFIELGKKDVYADASLGLAALAKSASFSVVDLDLNLKLQPARYRQLLQHILQHVADGKLEVLPVTAFSLHDAADAFRLMASGKHTGKIVISIPQHGSIEAIAAPPPLPLVSRDGGYLIVGGMGGLGFVVARWLAEQGAGLIVLNGRSAPSDEVAAAIAELNASGSRIEVITGDITEPDTAERLVRAVEDAGFRLAGVVHSAMVLADEIVLNMTDSAARRVFAPKVTGSWRLHVATAARDVDWWLTFSSAAALLGTPGQGAYAAANSWVDGLVAHRRSAGLPAVGINWGPWADVGRAQFFKDLGVEMINAEQGLAAMQAVLTADRGRTGVFSLDARQWFQSFPAVAGSSLFAKLHDSAARKSGQRRGGGAIRAQLDALDAAERPGHLASAIADEIRAVLRSGDPIDHHRPLETLGLDSLMGLELRNRLEASLGITLPVALVWAYPTISDLATALCERMDYATPAAAQEISDTEPELSDEEMDLLADLVDASELEAATRGES"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3255684", "fmax": "3262251", "strand": "+", "sequence": "ATGACCGCAGCGACACCAGATCGCCGAGCGATCATCACCGAGGCGCTGCACAAGATCGATGATCTCACGGCGCGCCTGGAAATCGCCGAAAAATCCAGCAGCGAACCGATCGCGGTGATCGGCATGGGTTGCCGGTTCCCGGGCGGGGTCAACAACCCCGAACAGTTCTGGGATTTGTTGTGCGCCGGCCGAAGCGGCATCGTCCGGGTTCCCGCGCAGCGGTGGGACGCCGACGCCTACTACTGTGATGATCACACCGTGCCGGGGACCATCTGCAGCACCGAAGGCGGTTTTCTCACCAGCTGGCAGCCAGATGAGTTCGATGCGGAGTTCTTCTCAATCTCCCCGCGCGAAGCGGCGGCGATGGACCCGCAGCAGCGATTGTTGATTGAAGTTGCGTGGGAAGCGCTAGAAGACGCGGGCGTCCCGCAACACACCATTCGCGGTACGCAAACCTCGGTATTCGTCGGTGTCACCGCCTACGACTACATGCTCACGCTGGCGGGCCGGCTACGACCTGTTGACCTCGACGCGTACATCCCAACCGGGAACTCGGCGAACTTCGCCGCCGGACGGCTGGCCTACATCCTCGGGGCACGCGGACCCGCGGTGGTCATCGACACGGCCTGCTCATCGTCGTTGGTGGCGGTGCACCTGGCATGCCAGAGCCTGCGCGGGCGGGAAAGCGATATGGCGTTGGTGGGTGGAACCAACCTTTTGCTGAGCCCGGGACCCAGCATCGCTTGCTCGCGATGGGGGATGCTGTCACCGGAGGGGCGGTGCAAGACCTTCGATGCGTCCGCCGATGGATACGTGCGCGGCGAGGGTGCCGCGGTGGTGGTGCTCAAGCGGCTGGATGACGCGGTGCGCGACGGCAACCGCATTCTTGCCGTGGTACGCGGTTCGGCGGTCAACCAGGACGGTGCCAGCAGCGGAGTGACCGTTCCCAACGGGCCAGCGCAACAGGCGTTGCTCGCCAAAGCATTGACGTCGTCGAAGTTGACAGCGGCCGATATCGACTACGTCGAGGCCCATGGAACTGGTACTCCGCTGGGCGACCCGATCGAACTCGATTCACTGAGTAAGGTTTTCAGCGATCGAGCGGGTTCGGATCAGTTGGTGATTGGATCGGTGAAGACCAATCTCGGTCACCTGGAAGCGGCGGCCGGTGTCGCCGGGCTGATGAAAGCCGTGCTCGCGGTACACAACGGCTACATTCCGCGGCATCTTAACTTCCACCAGCTGACACCACATGCAAGTGAGGCCGCATCTCGGCTGAGGATCGCCGCCGATGGTATTGACTGGCCAACCACCGGTCGACCTCGCCGGGCGGGGGTGTCGTCGTTCGGCGTCAGTGGGACGAATGCACACGTGGTGATCGAGCAGGCACCCGATCCGATGGCCGCTGCGGGAACGGAGCCGCAGCGCGGCCCCGTTCCCGCGGTGTCGACGCTGGTGGTGTTCGGCAAGACCGCACCGCGGGTGGCTGCGACGGCATCGGTGCTGGCAGATTGGCTGGACGGCCCCGGCGCGGCGGTGCCGCTGGCCGATGTCGCGCACACCCTCAACCATCACCGGGCCCGTCAGACCAGGTTCGGCACGGTAGCCGCTGTCGATCGGCGCCAAGCGGTGATCGGGTTACGCGCGCTGGCCGCGGGTCAATCCGCCCCCGGGGTGGTGGCACCCCGCGAAGGCTCCATCGGAGGCGGCACGGTGTTCGTCTACTCGGGACGAGGATCGCAGTGGGCCGGAATGGGGCGCCAACTGCTGGCCGACGAGCCGGCATTCGCCGCTGCCATCGCCGAACTGGAGCCGGAATTCGTTGCTCAAGGCGGGTTTTCGCTGCGCGACGTGATCGCCGGCGGAAAAGAGTTGGTTGGCATCGAACAGATCCAGCTGGGACTGATCGGGATGCAGCTGGCGCTGACCGCGTTGTGGCGCTCATACGGCGTGACACCCGATGCGGTGATAGGTCACTCGATGGGCGAAGTGGCCGCCGCGGTGGTGGCCGGGGCGCTGACCCCGGCCCAGGGATTACGGGTGACCGCGGTCCGGTCGAGGCTGATGGCGCCGCTGTCCGGGCAGGGCACGATGGCGTTGCTGGAACTCGACGCCGAAGCCACTGAGGCGCTGATTGCCGACTACCCCGAGGTGAGCCTGGGGATCTATGCCTCCCCACGCCAAACCGTGATTTCCGGGCCGCCGCTATTGATCGACGAGCTCATCGACAAGGTGCGCCAACAGAACGGCTTCGCTACCCGAGTCAACATCGAGGTGGCCCCCCACAACCCGGCCATGGATGCACTGCAACCGGCGATGCGTTCGGAATTGGCCGATCTCACCCCGCAACCGCCGACCATCCCGATCATCTCCACCACCTACGCCGACCTCGGCATTTCCCTGGGTTCCGGCCCCAGGTTCGACGCCGAGCACTGGGCAACCAACATGCGCAACCCGGTACGGTTCCACCAGGCCATCGCTCATGCCGGCGCCGATCACCACACCTTCATCGAGATCAGCGCCCACCCGCTGCTGACCCACTCGATCAGCGACACCCTGCGCGCCAGCTACGATGTCGACAACTATCTGAGCATCGGCACCTTGCAACGCGACGCTCACGACACCCTCGAGTTCCACACGAACCTCAACACGACCCACACCACCCATCCCCCCCAGACTCCCCACCCCCCCGAACCCCACCCCGTGCTGCCCACCACCCCATGGCAGCACACCCAGCACTGGATCACCGCCACGTCGGCCGCTTACCACAGGCCCGACACCCACCCGTTGCTTGGCGTCGGTGTCACCGACCCCACTAACGGCACCCGGGTTTGGGAAAGCGAGCTCGACCCTGATCTGCTGTGGCTCGCCGATCACGTCATCGACGATCTCGTTGTGCTGCCCGGGGCGGCCTACGCTGAGATCGCGCTGGCGGCCGCGACCGACACCTTCGCAGTCGAGCAAGATCAGCCCTGGATGATCAGCGAGCTCGACCTTCGGCAGATGCTGCATGTGACCCCAGGCACCGTGTTGGTCACCACGCTCACCGGCGACGAGCAGCGATGCCAGGTCGAAATACGCACCCGCAGCGGGTCTTCGGGATGGACCACCCACGCCACCGCCACCGTTGCCCGCGCCGAGCCGTTAGCACCGCTGGATCACGAAGGACAGCGGCGCGAGGTAACCACTGCCGACCTCGAGGACCAACTGGATCCCGACGACCTGTATCAGCGCCTGCGCGGCGCCGGCCAACAGCACGGACCCGCGTTTCAAGGCATCGTGGGGCTGGCCGTCACGCAAGCTGGCGTGGCCCGTGCGCAAGTACGGCTACCCGCATCGGCCAGAACGGGTTCCCGTGAGTTCATGCTGCACCCGGTGATGATGGATATCGCGTTGCAGACACTGGGAGCCACCCGGACGGCGACCGATCTGGCCGGCGGCCAGGACGCCCGGCAGGGCCCATCTTCCAACTCGGCCTTGGTGGTACCGGTGCGTTTCGCCGGTGTCCACGTGTACGGCGATATCACCCGCGGGGTTCGCGCGGTCGGCTCTCTGGCCGCAGCCGGTGACCGGCTGGTCGGCGAGGTAGTCCTGACCGACGCGAATGGCCAACCGCTGCTGGTCGTCGATGAAGTCGAGATGGCGGTGCTCGGATCCGGCAGTGGCGCAACGGAACTCACCAACCGCCTATTCATGTTGGAGTGGGAGCCCGCACCGCTGGAAAAGACCGCCGAGGCTACGGGTGCCCTGTTGCTGATCGGTGACCCCGCCGCGGGTGACCCGCTGCTGCCCGCGCTGCAGTCGTCGCTGCGCGACCGCATCACCGACCTCGAGCTGGCATCCGCGGCCGACGAAGCCACGCTGCGCGCGGCGATCAGCCGAACCTCCTGGGACGGGATCGTTGTGGTCTGTCCGCCCCGAGCGAACGACGAATCGATGCCGGACGAGGCTCAACTGGAGTTGGCACGCACACGCACGCTGCTGGTCGCCAGCGTGGTCGAGACCGTGACGCGAATGGGTGCCCGCAAGAGCCCCCGACTGTGGATCGTCACCCGTGGCGCTGCACAGTTCGACGCAGGCGAGTCGGTCACGTTGGCGCAGACCGGCCTACGTGGCATCGCACGGGTGCTGACATTTGAGCATTCGGAGTTGAATACCACCCTCGTAGATATCGAACCGGACGGCACCGGCTCGCTGGCCGCCCTGGCCGAGGAGTTGCTTGCCGGTTCCGAGGCCGACGAGGTCGCCTTGCGCGACGGTCAACGCTATGTCAACCGGCTGGTGCCCGCACCCACCACGACCAGTGGTGATCTCGCCGCCGAAGCTCGCCACCAGGTGGTGAACCTGGACAGCTCGGGCGCTTCCAGGGCAGCTGTCCGACTGCAGATCGATCAACCCGGACGGCTGGACGCACTAAACGTTCACGAGGTGAAACGGGGCAGACCGCAAGGCGATCAAGTCGAGGTTCGCGTCGTCGCCGCCGGACTCAACTTCAGCGACGTGCTCAAAGCGATGGGCGTGTATCCGGGACTCGACGGTGCCGCGCCGGTGATCGGCGGCGAATGTGTCGGCTACGTGACGGCCATCGGTGACGAGGTTGACGGCGTCGAGGTCGGACAGCGAGTTATCGCATTCGGCCCTGGCACATTCGGGACCCATCTGGGGACCATCGCCGATCTCGTCGTCCCAATTCCGGACACGCTAGCCGACAACGAGGCGGCCACGTTCGGCGTCGCCTATCTCACCGCCTGGCACTCGCTGTGCGAGGTCGGGCGCCTATCCCCCGGCGAACGCGTGCTCATCCATTCCGCCACCGGCGGTGTTGGAATGGCGGCGGTCTCGATCGCGAAGATGATCGGCGCCCGCATCTACACGACGGCCGGTTCGGACGCCAAACGGGAAATGCTTTCCAGGCTCGGTGTCGAGTACGTCGGCGACTCGCGAAGCGTGGATTTCGCTGACGAGATCCTCGAGCTGACAGACGGCTACGGTGTGGACGTCGTTCTCAATTCGCTGGCGGGCGAGGCGATTCAACGCGGCGTGCAGATCCTTGCGCCCGGTGGCCGGTTCATCGAACTGGGCAAGAAGGACGTCTACGCCGATGCCAGCTTGGGCTTGGCCGCGCTAGCCAAGAGCGCGTCCTTCTCCGTGGTCGACCTCGACCTGAATCTCAAGCTGCAGCCGGCGCGCTACCGCCAACTCCTGCAACACATCCTGCAGCACGTGGCGGATGGCAAACTCGAGGTACTTCCCGTCACCGCATTTAGCCTGCACGATGCGGCCGACGCATTCCGGCTTATGGCATCCGGTAAACACACCGGCAAGATCGTCATCTCGATACCCCAGCACGGCAGCATCGAGGCGATCGCTGCCCCGCCACCACTTCCTCTGGTCAGCCGCGACGGCGGCTACCTCATCGTCGGCGGTATGGGTGGTCTCGGATTCGTCGTCGCGCGCTGGCTGGCTGAGCAAGGTGCGGGACTGATTGTCCTCAACGGACGCTCGGCCCCCAGCGACGAGGTGGCAGCCGCTATCGCGGAGCTGAACGCCTCCGGTAGCCGGATCGAGGTGATCACCGGCGACATCACCGAGCCAGACACCGCCGAGCGGCTGGTGCGGGCGGTCGAAGACGCCGGGTTCCGGCTGGCCGGGGTGGTGCACAGCGCGATGGTTCTCGCCGACGAGATCGTGTTGAACATGACCGATTCCGCCGCTCGGCGAGTGTTCGCCCCGAAGGTCACCGGCAGCTGGCGGCTTCATGTGGCCACCGCCGCGCGCGACGTCGACTGGTGGCTGACCTTCTCCTCGGCCGCCGCGCTGCTGGGCACTCCCGGGCAGGGCGCGTACGCCGCCGCCAACTCGTGGGTCGACGGCCTGGTCGCGCATCGGCGCTCGGCCGGACTTCCCGCTGTCGGGATCAACTGGGGCCCGTGGGCCGACGTTGGACGCGCGCAGTTCTTCAAAGACCTCGGGGTGGAGATGATCAACGCCGAGCAGGGGCTTGCCGCCATGCAGGCGGTACTCACCGCCGATCGCGGGCGCACCGGTGTGTTCAGCCTCGACGCGCGGCAGTGGTTCCAATCGTTCCCCGCTGTGGCGGGGTCCTCGCTGTTCGCGAAGCTGCATGACTCGGCGGCCCGCAAAAGTGGGCAGCGGCGCGGCGGGGGCGCGATTCGCGCTCAGCTAGACGCCCTCGACGCGGCCGAACGCCCAGGCCACCTCGCGTCCGCGATCGCCGACGAGATCCGTGCGGTGCTGCGCTCAGGCGATCCCATCGATCACCACCGACCGCTGGAAACCCTGGGACTCGACTCGCTGATGGGCCTGGAATTGCGCAATCGGCTGGAAGCAAGTCTGGGCATCACGTTGCCGGTCGCGTTGGTGTGGGCATACCCGACGATCAGCGATCTCGCGACCGCCCTGTGCGAACGAATGGACTACGCGACACCCGCGGCTGCGCAGGAGATTTCCGATACAGAACCCGAACTGTCCGACGAGGAGATGGATTTGCTCGCCGATCTGGTTGACGCCAGCGAGCTGGAAGCTGCGACGCGAGGCGAGTCATGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004975", "ARO_id": "43162", "ARO_name": "Mycobacterium tuberculosis ppsC mutations confer resistance to pyrazinamide", "CARD_short_name": "Mtub_ppsC_PZA", "ARO_description": "Mutations in ppsC can contribute to or confer resistance to pyrazinamide.", "ARO_category": {"43189": {"category_aro_accession": "3005002", "category_aro_cvterm_id": "43189", "category_aro_name": "antibiotic resistant polyketide synthase genes", "category_aro_description": "Genes ppsA-E constitute an operon encoding enzymes involved in the biosynthesis of phthiocerol dimycocerosate and other lipids in Mycobacterium tuberculosis. Mutations within this region can result in resistance to pyrazinamide.", "category_aro_class_name": "AMR Gene Family"}, "39997": {"category_aro_accession": "3003413", "category_aro_cvterm_id": "39997", "category_aro_name": "pyrazinamide", "category_aro_description": "Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.", "category_aro_class_name": "Antibiotic"}, "45737": {"category_aro_accession": "3007155", "category_aro_cvterm_id": "45737", "category_aro_name": "pyrazine antibiotic", "category_aro_description": "A group of antibiotics derived from pyrazine.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3738": {"model_id": "3738", "model_name": "Mycobacterium tuberculosis mshC mutations conferring resistance to ethionamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9518": "A403G"}, "clinical": {"9518": "A403G"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "775"}}, "model_sequences": {"sequence": {"8838": {"protein_sequence": {"accession": "NP_216646.1", "sequence": "MQSWYCPPVPVLPGRGPQLRLYDSADRQVRPVAPGSKATMYVCGITPYDATHLGHAATYVTFDLIHRLWLDLGHELHYVQNITDIDDPLFERADRDGVDWRDLAQAEVALFCEDMAALRVLPPQDYVGATEAIAEMVELIEKMLACGAAYVIDREMGEYQDIYFRADATLQFGYESGYDRDTMLRLCEERGGDPRRPGKSDELDALLWRAARPGEPSWPSPFGPGRPGWHVECAAIALSRIGSGLDIQGGGSDLIFPHHEFTAAHAECVSGERRFARHYVHAGMIGWDGHKMSKSRGNLVLVSALRAQDVEPSAVRLGLLAGHYRADRFWSQQVLDEATARLHRWRTATALPAGPAAVDVVARVRRYLADDLDTPKAIAALDGWVTDAVEYGGHDAGAPKLVATAIDALLGVDL"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "2391214", "fmax": "2392459", "strand": "-", "sequence": "ATGCAGTCGTGGTATTGCCCACCGGTTCCGGTGTTGCCGGGACGAGGCCCGCAGCTACGGCTGTACGACAGCGCCGACCGGCAGGTCCGTCCGGTGGCGCCCGGATCTAAGGCCACCATGTACGTCTGCGGGATCACGCCCTACGACGCCACGCATCTGGGCCATGCTGCCACCTATGTGACGTTCGACCTGATCCATCGGCTGTGGCTGGATCTCGGTCATGAATTGCACTATGTCCAGAACATCACCGACATCGACGATCCACTATTTGAGCGCGCGGATCGCGACGGTGTCGACTGGCGTGACCTTGCCCAAGCCGAGGTCGCCCTGTTCTGTGAGGACATGGCGGCGCTGCGGGTGCTACCACCGCAAGACTACGTGGGGGCCACCGAAGCGATTGCTGAAATGGTCGAGCTCATCGAAAAAATGCTGGCGTGCGGGGCGGCCTATGTCATAGACCGGGAAATGGGAGAGTACCAGGACATCTACTTCCGCGCTGACGCCACCCTGCAGTTCGGCTACGAGTCAGGGTATGACCGTGACACCATGCTGCGGCTGTGCGAGGAACGTGGCGGCGATCCGCGGCGCCCCGGCAAGAGCGACGAACTCGACGCGTTGTTGTGGCGGGCCGCGCGGCCCGGTGAGCCCAGCTGGCCGTCCCCGTTCGGGCCTGGCCGGCCAGGCTGGCATGTCGAGTGCGCAGCCATCGCGCTCAGTCGTATCGGAAGCGGCCTCGACATCCAGGGCGGTGGTAGCGATCTGATCTTTCCGCACCACGAGTTCACCGCTGCGCACGCCGAATGTGTCAGCGGCGAACGGCGATTCGCGCGGCACTACGTGCATGCCGGGATGATCGGCTGGGACGGGCACAAGATGTCAAAGAGCCGCGGCAACCTCGTGCTGGTGTCGGCGCTGCGTGCGCAGGACGTTGAGCCATCGGCGGTTCGGCTGGGTTTGCTCGCCGGACACTACCGAGCCGATCGGTTCTGGAGCCAGCAGGTGCTTGACGAGGCGACCGCCCGGCTGCACCGTTGGCGCACCGCAACCGCACTTCCCGCCGGTCCGGCCGCAGTTGACGTTGTCGCTCGGGTGCGCCGCTACCTGGCCGACGATCTCGATACGCCCAAAGCGATTGCCGCACTGGATGGTTGGGTCACCGATGCGGTGGAGTACGGCGGCCACGATGCCGGGGCGCCGAAGTTGGTGGCGACGGCGATCGATGCCCTGCTCGGGGTGGACCTGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004934", "ARO_id": "43120", "ARO_name": "Mycobacterium tuberculosis mshC mutations conferring resistance to ethionamide", "CARD_short_name": "Mtub_mshC_ETO", "ARO_description": "Mutations that occur in mshC resulting in or contributing to conferring resistance to ethionamide.", "ARO_category": {"43076": {"category_aro_accession": "3004890", "category_aro_cvterm_id": "43076", "category_aro_name": "ethionamide resistant mshC", "category_aro_description": "Mutations that occur in mshC which is involved in the third step of mycothiol biosynthesis. It catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins. The gene exhibits resistance to ethionamide.", "category_aro_class_name": "AMR Gene Family"}, "40067": {"category_aro_accession": "3003474", "category_aro_cvterm_id": "40067", "category_aro_name": "ethionamide", "category_aro_description": "Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.", "category_aro_class_name": "Antibiotic"}, "45738": {"category_aro_accession": "3007156", "category_aro_cvterm_id": "45738", "category_aro_name": "thioamide antibiotic", "category_aro_description": "A group of antibiotics possessing the thioamide functional group.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3713": {"model_id": "3713", "model_name": "Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9709": "A437P", "9710": "P563H", "9711": "A1248T", "9713": "M127I", "9714": "I1508L", "9715": "V1522A", "9717": "E1823A", "9718": "V295M"}, "clinical": {"9709": "A437P", "9710": "P563H", "9711": "A1248T", "9713": "M127I", "9714": "I1508L", "9715": "V1522A", "9717": "E1823A", "9718": "V295M"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "3575"}}, "model_sequences": {"sequence": {"8793": {"protein_sequence": {"accession": "NP_217450.1", "sequence": "MTSLAERAAQLSPNARAALARELVRAGTTFPTDICEPVAVVGIGCRFPGNVTGPESFWQLLADGVDTIEQVPPDRWDADAFYDPDPSASGRMTTKWGGFVSDVDAFDADFFGITPREAVAMDPQHRMLLEVAWEALEHAGIPPDSLSGTRTGVMMGLSSWDYTIVNIERRADIDAYLSTGTPHCAAVGRIAYLLGLRGPAVAVDTACSSSLVAIHLACQSLRLRETDVALAGGVQLTLSPFTAIALSKWSALSPTGRCNSFDANADGFVRGEGCGVVVLKRLADAVRDQDRVLAVVRGSATNSDGRSNGMTAPNALAQRDVITSALKLADVTPDSVNYVETHGTGTVLGDPIEFESLAATYGLGKGQGESPCALGSVKTNIGHLEAAAGVAGFIKAVLAVQRGHIPRNLHFTRWNPAIDASATRLFVPTESAPWPAAAGPRRAAVSSFGLSGTNAHVVVEQAPDTAVAAAGGMPYVSALNVSGKTAARVASAAAVLADWMSGPGAAAPLADVAHTLNRHRARHAKFATVIARDRAEAIAGLRALAAGQPRVGVVDCDQHAGGPGRVFVYSGQGSQWASMGQQLLANEPAFAKAVAELDPIFVDQVGFSLQQTLIDGDEVVGIDRIQPVLVGMQLALTELWRSYGVIPDAVIGHSMGEVSAAVVAGALTPEQGLRVITTRSRLMARLSGQGAMALLELDADAAEALIAGYPQVTLAVHASPRQTVIAGPPEQVDTVIAAVATQNRLARRVEVDVASHHPIIDPILPELRSALADLTPQPPSIPIISTTYESAQPVADADYWSANLRNPVRFHQAVTAAGVDHNTFIEISPHPVLTHALTDTLDPDGSHTVMSTMNRELDQTLYFHAQLAAVGVAASEHTTGRLVDLPPTPWHHQRFWVTDRSAMSELAATHPLLGAHIEMPRNGDHVWQTDVGTEVCPWLADHKVFGQPIMPAAGFAEIALAAASEALGTAADAVAPNIVINQFEVEQMLPLDGHTPLTTQLIRGGDSQIRVEIYSRTRGGEFCRHATAKVEQSPRECAHAHPEAQGPATGTTVSPADFYALLRQTGQHHGPAFAALSRIVRLADGSAETEISIPDEAPRHPGYRLHPVVLDAALQSVGAAIPDGEIAGSAEASYLPVSFETIRVYRDIGRHVRCRAHLTNLDGGTGKMGRIVLINDAGHIAAEVDGIYLRRVERRAVPLPLEQKIFDAEWTESPIAAVPAPEPAAETTRGSWLVLADATVDAPGKAQAKSMADDFVQQWRSPMRRVHTADIHDESAVLAAFAETAGDPEHPPVGVVVFVGGASSRLDDELAAARDTVWSITTVVRAVVGTWHGRSPRLWLVTGGGLSVADDEPGTPAAASLKGLVRVLAFEHPDMRTTLVDLDITQDPLTALSAELRNAGSGSRHDDVIAWRGERRFVERLSRATIDVSKGHPVVRQGASYVVTGGLGGLGLVVARWLVDRGAGRVVLGGRSDPTDEQCNVLAELQTRAEIVVVRGDVASPGVAEKLIETARQSGGQLRGVVHAAAVIEDSLVFSMSRDNLERVWAPKATGALRMHEATADCELDWWLGFSSAASLLGSPGQAAYACASAWLDALVGWRRASGLPAAVINWGPWSEVGVAQALVGSVLDTISVAEGIEALDSLLAADRIRTGVARLRADRALVAFPEIRSISYFTQVVEELDSAGDLGDWGGPDALADLDPGEARRAVTERMCARIAAVMGYTDQSTVEPAVPLDKPLTELGLDSLMAVRIRNGARADFGVEPPVALILQGASLHDLTADLMRQLGLNDPDPALNNADTIRDRARQRAAARHGAAMRRRPKPEVQGG"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3262247", "fmax": "3267731", "strand": "+", "sequence": "ATGACAAGTCTGGCGGAGCGCGCGGCGCAACTGTCGCCGAACGCGCGAGCGGCCCTGGCGCGCGAGCTCGTCCGTGCGGGTACGACCTTCCCGACCGACATCTGCGAGCCGGTGGCGGTGGTGGGCATCGGCTGTCGCTTTCCGGGGAATGTGACTGGGCCAGAGAGCTTTTGGCAGCTACTGGCCGACGGTGTGGACACAATCGAGCAGGTGCCGCCTGATCGGTGGGATGCGGACGCGTTCTACGATCCCGATCCTTCGGCGTCGGGTCGGATGACGACGAAATGGGGTGGTTTCGTTTCCGATGTCGACGCGTTCGACGCCGACTTTTTCGGAATCACTCCTCGGGAAGCCGTGGCGATGGACCCGCAGCATCGGATGCTGCTCGAGGTTGCCTGGGAAGCGTTGGAGCACGCGGGTATTCCGCCGGATTCCTTGAGCGGCACTCGAACCGGCGTGATGATGGGTCTGTCGTCGTGGGACTACACGATCGTCAATATCGAGCGCAGAGCCGACATCGACGCGTACCTGAGCACCGGAACCCCGCACTGTGCCGCGGTGGGGCGGATCGCGTATCTGTTGGGATTGCGTGGTCCGGCCGTCGCCGTAGATACCGCTTGTTCGTCGTCGCTGGTGGCAATTCACTTGGCGTGTCAGAGCCTTCGCCTGCGTGAAACCGACGTGGCATTGGCGGGCGGGGTGCAGCTCACCTTGTCACCGTTCACCGCCATCGCGCTGTCCAAGTGGTCGGCGCTGTCACCGACCGGCCGATGCAACAGCTTCGACGCCAACGCGGATGGATTCGTGCGCGGCGAGGGCTGCGGCGTGGTGGTGCTCAAGCGGTTGGCCGACGCGGTGCGCGACCAGGACCGGGTGCTTGCGGTGGTCCGCGGTTCGGCAACTAACTCCGATGGTCGGTCCAACGGCATGACCGCACCGAACGCGCTGGCGCAGCGTGACGTGATCACATCCGCCCTCAAGCTTGCGGATGTTACCCCTGACAGCGTGAACTATGTCGAAACACACGGCACCGGAACGGTGTTGGGGGACCCCATCGAGTTCGAGTCGCTGGCGGCCACTTATGGCCTGGGTAAAGGCCAGGGCGAGAGCCCGTGCGCATTGGGGTCGGTCAAGACCAACATCGGCCACCTGGAGGCGGCCGCCGGTGTGGCTGGATTCATCAAGGCGGTGCTGGCGGTGCAACGTGGGCACATTCCCCGCAACTTGCACTTCACCCGGTGGAACCCGGCCATCGACGCGTCGGCGACGCGGCTGTTCGTGCCGACCGAAAGCGCCCCGTGGCCGGCGGCTGCCGGTCCACGCAGGGCTGCGGTGTCATCGTTCGGCCTCAGCGGGACCAACGCGCACGTGGTGGTCGAGCAGGCACCCGACACCGCAGTAGCCGCAGCCGGCGGCATGCCGTATGTTTCGGCGCTGAACGTCTCCGGCAAGACGGCCGCGCGGGTGGCGTCGGCGGCGGCGGTGCTGGCCGACTGGATGTCGGGGCCGGGCGCGGCGGCACCACTGGCCGACGTGGCACACACGTTGAACCGGCACCGGGCCCGGCACGCCAAGTTCGCCACCGTCATCGCGCGTGACCGCGCCGAGGCGATCGCGGGGTTGCGAGCGCTGGCGGCCGGACAACCACGCGTTGGGGTGGTGGATTGCGACCAGCATGCCGGTGGGCCTGGCCGGGTTTTTGTGTATTCGGGTCAGGGCTCGCAGTGGGCGTCGATGGGCCAGCAGTTGCTGGCCAACGAACCGGCGTTCGCCAAGGCGGTAGCCGAGCTGGATCCGATATTCGTTGACCAGGTTGGCTTTTCGCTGCAGCAAACGCTTATCGACGGCGACGAGGTGGTGGGCATCGACCGCATCCAGCCGGTGCTGGTCGGGATGCAGTTGGCGCTGACCGAGTTATGGCGGTCCTATGGGGTGATTCCAGATGCCGTGATCGGGCACTCGATGGGTGAGGTGTCGGCGGCAGTGGTGGCCGGCGCGTTGACGCCCGAGCAGGGCTTGCGGGTCATCACCACCCGGTCGCGGTTGATGGCGCGGCTGTCGGGGCAGGGAGCGATGGCGCTGCTCGAGCTGGATGCCGACGCCGCCGAGGCGCTGATTGCCGGCTATCCGCAGGTGACGCTGGCGGTGCATGCGTCACCGCGCCAGACGGTGATCGCCGGGCCGCCCGAGCAGGTGGACACGGTGATCGCGGCGGTAGCGACGCAAAACCGGTTGGCGCGCCGCGTCGAAGTCGACGTGGCCTCCCATCACCCGATCATCGATCCCATACTGCCCGAGTTGCGAAGCGCGTTAGCGGATTTGACTCCGCAGCCGCCGAGCATCCCGATCATTTCCACTACGTACGAAAGCGCGCAGCCGGTGGCGGATGCCGACTATTGGTCGGCCAACCTGCGCAACCCGGTGCGATTCCACCAGGCCGTCACCGCCGCCGGTGTCGACCACAACACCTTCATCGAAATCAGCCCTCACCCCGTGCTCACGCACGCACTCACCGACACCCTGGATCCGGACGGCAGCCATACAGTCATGTCGACGATGAACCGCGAACTGGACCAGACGCTGTATTTCCACGCCCAACTCGCCGCGGTCGGTGTGGCTGCGTCCGAGCACACCACCGGTCGCCTTGTCGACCTGCCCCCCACACCGTGGCACCATCAGCGATTCTGGGTCACGGATCGTTCGGCGATGTCCGAGCTGGCCGCGACCCACCCGCTCCTGGGCGCGCACATCGAGATGCCGCGCAACGGAGACCATGTCTGGCAGACCGATGTCGGCACCGAGGTCTGTCCCTGGTTGGCAGACCACAAGGTGTTCGGTCAACCCATCATGCCGGCCGCGGGGTTCGCCGAGATCGCCTTGGCGGCGGCCAGCGAAGCCCTCGGCACAGCCGCCGACGCCGTCGCACCCAACATCGTGATCAACCAGTTCGAGGTGGAGCAGATGCTGCCCCTCGACGGCCACACGCCGCTAACGACGCAGTTAATTCGCGGCGGGGACAGCCAGATTCGGGTCGAGATCTATTCCCGCACGCGTGGCGGAGAGTTCTGCCGACACGCCACGGCCAAGGTTGAACAATCGCCGCGCGAATGTGCGCACGCGCACCCGGAAGCCCAAGGTCCCGCCACCGGGACAACAGTGTCGCCGGCCGATTTTTATGCCCTGCTCCGCCAAACCGGCCAACACCATGGTCCGGCGTTCGCGGCCTTAAGCCGGATCGTGCGCCTGGCCGATGGTTCCGCGGAAACCGAGATCAGCATTCCCGACGAGGCGCCGCGCCATCCCGGGTATCGGCTGCACCCCGTGGTATTGGATGCGGCATTGCAAAGCGTGGGTGCCGCGATACCCGACGGCGAGATCGCGGGGTCGGCGGAAGCCAGCTATCTGCCAGTGTCGTTCGAGACCATCCGGGTGTACCGCGACATCGGTCGGCACGTCAGGTGTCGTGCCCACCTGACAAACCTCGACGGCGGCACCGGAAAGATGGGCAGGATCGTCCTAATCAACGACGCCGGCCACATAGCGGCCGAAGTGGACGGCATCTATCTGCGTCGTGTCGAACGCCGTGCGGTACCCCTGCCACTAGAGCAGAAGATCTTCGATGCCGAATGGACCGAAAGCCCGATCGCAGCCGTGCCGGCTCCGGAGCCAGCTGCCGAGACGACGCGGGGAAGTTGGCTGGTACTCGCCGATGCAACGGTGGATGCGCCAGGCAAGGCCCAGGCCAAGTCGATGGCCGACGACTTCGTGCAGCAGTGGCGCTCACCGATGCGGCGGGTGCACACCGCCGATATCCACGACGAATCGGCGGTGCTGGCCGCATTTGCAGAAACGGCAGGCGATCCCGAGCACCCGCCGGTTGGCGTGGTGGTGTTCGTCGGCGGTGCCTCGAGTCGACTGGACGACGAGCTGGCGGCGGCGCGCGACACGGTGTGGTCGATCACCACGGTGGTTCGTGCGGTCGTCGGCACGTGGCACGGCCGATCACCGCGGCTATGGCTGGTCACCGGGGGCGGACTTTCCGTTGCCGACGACGAGCCGGGAACACCCGCGGCGGCTTCCTTGAAAGGGCTGGTGCGGGTGCTCGCCTTCGAGCACCCGGACATGCGCACCACCCTGGTCGATCTGGACATCACACAAGACCCGCTGACCGCGCTGAGCGCGGAACTGCGGAATGCCGGGAGTGGGTCGCGCCATGATGACGTGATCGCGTGGCGCGGCGAGCGCAGGTTCGTCGAACGGCTGTCGCGCGCCACGATCGATGTATCCAAAGGGCATCCGGTGGTGCGCCAGGGAGCGTCGTACGTCGTCACCGGCGGCCTCGGCGGTCTCGGCCTGGTCGTCGCTCGTTGGCTGGTGGACCGCGGCGCCGGCCGGGTGGTGCTGGGTGGCCGCAGCGATCCCACTGACGAGCAGTGCAACGTCCTGGCCGAACTGCAGACCCGCGCCGAGATCGTGGTTGTCCGTGGCGACGTGGCATCGCCGGGGGTGGCAGAAAAGCTGATTGAGACGGCCCGACAGTCTGGGGGCCAATTGCGCGGCGTCGTGCACGCCGCCGCGGTCATCGAAGACAGCCTGGTGTTCTCTATGAGCAGGGACAACCTAGAACGGGTGTGGGCACCCAAGGCCACCGGTGCGCTGCGCATGCACGAAGCCACCGCTGACTGCGAGCTCGACTGGTGGCTCGGATTCTCTTCCGCCGCTTCGCTATTGGGTTCTCCCGGGCAAGCGGCCTACGCGTGCGCCAGCGCGTGGCTGGACGCGCTGGTCGGATGGCGCAGGGCATCCGGCCTGCCGGCCGCGGTGATCAACTGGGGTCCGTGGTCGGAGGTAGGCGTCGCCCAGGCCTTGGTGGGCAGTGTTCTCGACACGATCAGTGTCGCAGAAGGCATCGAGGCTCTCGACTCATTGCTTGCCGCCGACCGGATCCGCACTGGAGTGGCTCGGCTGCGTGCCGATCGGGCCCTGGTCGCATTCCCGGAGATCCGCAGCATCAGCTACTTCACCCAGGTGGTCGAGGAGCTGGACTCGGCGGGTGACCTCGGCGACTGGGGCGGGCCCGACGCGCTTGCCGACCTCGACCCGGGCGAGGCGCGGCGCGCGGTGACCGAGCGGATGTGTGCGCGCATCGCTGCGGTGATGGGCTACACTGACCAGTCGACTGTCGAACCCGCCGTGCCCTTGGACAAGCCCCTGACCGAGCTGGGGCTGGATTCTCTGATGGCGGTACGAATACGCAACGGCGCGCGGGCGGATTTCGGCGTGGAACCGCCGGTAGCGCTGATACTGCAAGGCGCGTCCTTGCATGACCTGACGGCGGACTTAATGCGCCAACTCGGGCTCAATGATCCCGATCCGGCGCTCAACAACGCTGACACTATTCGCGACCGGGCGCGCCAGCGCGCGGCAGCGCGACACGGAGCCGCGATGCGGCGCCGACCTAAACCTGAAGTACAGGGAGGATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004976", "ARO_id": "43163", "ARO_name": "Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide", "CARD_short_name": "Mtub_ppsD_PZA", "ARO_description": "Mutations in ppsD can contribute to or confer resistance to pyrazinamide.", "ARO_category": {"43189": {"category_aro_accession": "3005002", "category_aro_cvterm_id": "43189", "category_aro_name": "antibiotic resistant polyketide synthase genes", "category_aro_description": "Genes ppsA-E constitute an operon encoding enzymes involved in the biosynthesis of phthiocerol dimycocerosate and other lipids in Mycobacterium tuberculosis. Mutations within this region can result in resistance to pyrazinamide.", "category_aro_class_name": "AMR Gene Family"}, "39997": {"category_aro_accession": "3003413", "category_aro_cvterm_id": "39997", "category_aro_name": "pyrazinamide", "category_aro_description": "Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.", "category_aro_class_name": "Antibiotic"}, "45737": {"category_aro_accession": "3007155", "category_aro_cvterm_id": "45737", "category_aro_name": "pyrazine antibiotic", "category_aro_description": "A group of antibiotics derived from pyrazine.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3723": {"model_id": "3723", "model_name": "Mycobacterium tuberculosis ahpC mutations confer resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"41339": {"param_type": "snp in promoter region", "param_description": "A SNP in the promoter region of a gene which alters transcription of that gene, encoded as [wild-type][-][position][mutation], for example t-11c. Var represents any possible substitution. This is a pilot parameter in need of further documentation.", "param_type_id": "41339", "param_value": {"13291": "c-72t", "13343": "g-48a", "13687": "c-57t"}}, "41345": {"param_type": "insertion mutation from nucleotide sequence", "param_description": "A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG or +nt368:18. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.", "param_type_id": "41345", "param_value": {"9526": "+nt47:t"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"13006": "C52T", "13007": "C72T", "13008": "C81T", "13009": "G48A"}, "clinical": {"13006": "C52T", "13007": "C72T", "13008": "C81T", "13009": "G48A"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "325"}}, "model_sequences": {"sequence": {"8771": {"protein_sequence": {"accession": "NP_216944.1", "sequence": "MPLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQSDELCACNWRKGDPTLDAGELLKASA"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "2726192", "fmax": "2726780", "strand": "+", "sequence": "ATGCCACTGCTAACCATTGGCGATCAATTCCCCGCCTACCAGCTCACCGCTCTCATCGGCGGTGACCTGTCCAAGGTCGACGCCAAGCAGCCCGGCGACTACTTCACCACTATCACCAGTGACGAACACCCAGGCAAGTGGCGGGTGGTGTTCTTTTGGCCGAAAGACTTCACGTTCGTGTGCCCTACCGAGATCGCGGCGTTCAGCAAGCTCAATGACGAGTTCGAGGACCGCGACGCCCAGATCCTGGGGGTTTCGATTGACAGCGAATTCGCGCATTTCCAGTGGCGTGCACAGCACAACGACCTCAAAACGTTACCCTTCCCGATGCTCTCCGACATCAAGCGCGAACTCAGCCAAGCCGCAGGTGTCCTCAACGCCGACGGTGTGGCCGACCGCGTGACCTTTATCGTCGACCCCAACAACGAGATCCAGTTCGTCTCGGCCACCGCCGGTTCGGTGGGACGCAACGTCGATGAGGTACTGCGAGTGCTCGACGCCCTCCAGTCCGACGAGCTGTGCGCATGCAACTGGCGCAAGGGCGACCCGACGCTAGACGCTGGCGAACTCCTCAAGGCTTCGGCCTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004921", "ARO_id": "43107", "ARO_name": "Mycobacterium tuberculosis ahpC mutations confer resistance to isoniazid", "CARD_short_name": "Mtub_ahpC_INH", "ARO_description": "Mutations that occur in ahpC that result in ahpC overexpression thus conferring or contributing to resistance to isoniazid.", "ARO_category": {"43080": {"category_aro_accession": "3004894", "category_aro_cvterm_id": "43080", "category_aro_name": "Isoniazid resistant ahpC", "category_aro_description": "An alkyl hydroperoxide reductase that catalyzes the reduction of organic hydrogen peroxide to water and organic alcohols. Plays a role in protecting oxidative stress.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3724": {"model_id": "3724", "model_name": "Mycobacterium tuberculosis fabG1 mutations confer resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"41339": {"param_type": "snp in promoter region", "param_description": "A SNP in the promoter region of a gene which alters transcription of that gene, encoded as [wild-type][-][position][mutation], for example t-11c. Var represents any possible substitution. This is a pilot parameter in need of further documentation.", "param_type_id": "41339", "param_value": {"13398": "c-15t", "13399": "g-17t", "13400": "t-8c", "14181": "c-15Var", "14182": "t-8Var", "14180": "a-16Var", "14765": "g-17t", "14767": "c-15t", "14769": "a-16g", "14771": "t-8c", "14773": "t-8g", "14775": "t-8a"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"13700": "L203L"}, "clinical": {"13700": "L203L"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "425"}}, "model_sequences": {"sequence": {"8815": {"protein_sequence": {"accession": "NP_215999.1", "sequence": "MTATATEGAKPPFVSRSVLVTGGNRGIGLAIAQRLAADGHKVAVTHRGSGAPKGLFGVECDVTDSDAVDRAFTAVEEHQGPVEVLVSNAGLSADAFLMRMTEEKFEKVINANLTGAFRVAQRASRSMQRNKFGRMIFIGSVSGSWGIGNQANYAASKAGVIGMARSIARELSKANVTANVVAPGYIDTDMTRALDERIQQGALQFIPAKRVGTPAEVAGVVSFLASEDASYISGAVIPVDGGMGMGH"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "1673439", "fmax": "1674183", "strand": "+", "sequence": "GTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCCCGTTCAGTCCTGGTTACCGGAGGAAACCGGGGGATCGGGCTGGCGATCGCACAGCGGCTGGCTGCCGACGGCCACAAGGTGGCCGTCACCCACCGTGGATCCGGAGCGCCAAAGGGGCTGTTTGGCGTCGAATGTGACGTCACCGACAGCGACGCCGTCGATCGCGCCTTCACGGCGGTAGAAGAGCACCAGGGTCCGGTCGAGGTGCTGGTGTCCAACGCCGGCCTATCCGCGGACGCATTCCTCATGCGGATGACCGAGGAAAAGTTCGAGAAGGTCATCAACGCCAACCTCACCGGGGCGTTCCGGGTGGCTCAACGGGCATCGCGCAGCATGCAGCGCAACAAATTCGGTCGAATGATATTCATAGGTTCGGTCTCCGGCAGCTGGGGCATCGGCAACCAGGCCAACTACGCAGCCTCCAAGGCCGGAGTGATTGGCATGGCCCGCTCGATCGCCCGCGAGCTGTCGAAGGCAAACGTGACCGCGAATGTGGTGGCCCCGGGCTACATCGACACCGATATGACCCGCGCGCTGGATGAGCGGATTCAGCAGGGGGCGCTGCAATTTATCCCAGCGAAGCGGGTCGGCACCCCCGCCGAGGTCGCCGGGGTGGTCAGCTTCCTGGCTTCCGAGGATGCGAGCTATATCTCCGGTGCGGTCATCCCGGTCGACGGCGGCATGGGTATGGGCCACTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004922", "ARO_id": "43108", "ARO_name": "Mycobacterium tuberculosis fabG1 mutations confer resistance to isoniazid", "CARD_short_name": "Mtub_fabG1_INH", "ARO_description": "Mutations that occur in fabG1 resulting in or contributing to resistance in isoniazid.", "ARO_category": {"43081": {"category_aro_accession": "3004895", "category_aro_cvterm_id": "43081", "category_aro_name": "isoniazid resistant fabG1", "category_aro_description": "fabG1 is involved in the fatty acid synthesis pathway, acting in the first reduction step for mycolic acid. It is associated with isoniazid resistance.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3740": {"model_id": "3740", "model_name": "Mycobacterium tuberculosis ubiA mutations confer resistance to ethambutol", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9500": "S173A", "9502": "A237V", "9503": "R240C", "9501": "W175C"}, "clinical": {"9500": "S173A", "9502": "A237V", "9503": "R240C", "9501": "W175C"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "525"}}, "model_sequences": {"sequence": {"8795": {"protein_sequence": {"accession": "NP_218323.1", "sequence": "MSEDVVTQPPANLVAGVVKAIRPRQWVKNVLVLAAPLAALGGGVRYDYVEVLSKVSMAFVVFSLAASAVYLVNDVRDVEADREHPTKRFRPIAAGVVPEWLAYTVAVVLGVTSLAGAWMLTPNLALVMVVYLAMQLAYCFGLKHQAVVEICVVSSAYLIRAIAGGVATKIPLSKWFLLIMAFGSLFMVAGKRYAELHLAERTGAAIRKSLESYTSTYLRFVWTLSATAVVLCYGLWAFERDGYSGSWFAVSMIPFTIAILRYAVDVDGGLAGEPEDIALRDRVLQLLALAWIATVGAAVAFG"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "4268924", "fmax": "4269833", "strand": "-", "sequence": "ATGAGTGAAGATGTGGTGACTCAACCTCCGGCAAACCTGGTCGCCGGGGTGGTCAAGGCGATCCGCCCGCGCCAGTGGGTGAAAAACGTGCTGGTGCTGGCCGCGCCGCTGGCCGCGTTGGGCGGCGGTGTCCGCTACGACTACGTCGAGGTGCTCAGCAAGGTGTCGATGGCCTTCGTGGTGTTCAGCCTGGCCGCCTCGGCGGTGTACCTCGTCAACGATGTGCGTGACGTCGAGGCAGACCGGGAGCACCCCACCAAAAGGTTCCGGCCGATCGCCGCCGGCGTGGTGCCCGAGTGGCTGGCGTACACCGTGGCGGTGGTACTGGGAGTGACATCGCTGGCCGGTGCCTGGATGCTGACCCCGAACCTGGCGCTGGTAATGGTCGTCTACCTCGCCATGCAGTTGGCGTATTGCTTTGGTCTCAAGCATCAAGCGGTGGTGGAAATCTGCGTCGTGTCGTCGGCGTATTTGATCCGCGCCATCGCCGGGGGCGTGGCCACCAAAATCCCGCTGTCCAAGTGGTTTTTGCTGATCATGGCATTCGGTTCGCTGTTCATGGTGGCCGGCAAGCGCTACGCCGAGCTGCATCTGGCCGAACGCACCGGCGCTGCGATCCGCAAGTCGCTGGAAAGCTACACCAGCACCTATCTGCGGTTCGTCTGGACGTTGTCGGCCACCGCGGTGGTCTTGTGCTACGGGCTGTGGGCTTTCGAGCGCGACGGCTACAGCGGGTCCTGGTTCGCGGTGTCGATGATTCCGTTCACCATCGCGATCCTGCGCTACGCGGTGGACGTCGATGGCGGCCTGGCCGGGGAGCCGGAAGATATCGCGCTGCGTGACCGGGTATTGCAGCTGCTGGCGCTGGCGTGGATAGCAACGGTTGGGGCCGCTGTTGCCTTCGGCTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004950", "ARO_id": "43136", "ARO_name": "Mycobacterium tuberculosis ubiA mutations confer resistance to ethambutol", "CARD_short_name": "Mtub_ubiA_EMB", "ARO_description": "Mutations in the ubiA gene contribute to or confer resistance to ethambutol.", "ARO_category": {"43135": {"category_aro_accession": "3004949", "category_aro_cvterm_id": "43135", "category_aro_name": "ethambutol resistant ubiA", "category_aro_description": "DDPR synthase involved in arabinogalactan synthesis. Mutations can confer resistance to ethambutol.", "category_aro_class_name": "AMR Gene Family"}, "36636": {"category_aro_accession": "3000497", "category_aro_cvterm_id": "36636", "category_aro_name": "ethambutol", "category_aro_description": "Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.", "category_aro_class_name": "Antibiotic"}, "36666": {"category_aro_accession": "3000527", "category_aro_cvterm_id": "36666", "category_aro_name": "polyamine antibiotic", "category_aro_description": "Polyamine antibiotics are organic compounds having two or more primary amino groups.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3715": {"model_id": "3715", "model_name": "Mycobacterium tuberculosis mas mutations confer resistance to pyrazinamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9639": "P398R", "9640": "P495R", "9642": "L98M", "9644": "T2005P", "9645": "S213C"}, "clinical": {"9639": "P398R", "9640": "P495R", "9642": "L98M", "9644": "T2005P", "9645": "S213C"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "4180"}}, "model_sequences": {"sequence": {"8835": {"protein_sequence": {"accession": "NP_217456.1", "sequence": "MESRVTPVAVIGMGCRLPGGINSPDKLWESLLRGDDLVTEIPPDRWDADDYYDPEPGVPGRSVSRWGGFLDDVAGFDAEFFGISEREATSIDPQQRLLLETSWEAIEHAGLDPASLAGSSTAVFTGLTHEDYLVLTTTAGGLASPYVVTGLNNSVASGRIAHTLGLHGPAMTFDTACSSGLMAVHLACRSLHDGEADLALAGGCAVLLEPHASVAASAQGMLSSTGRCHSFDADADGFVRSEGCAMVLLKRLPDALRDGNRIFAVVRGTATNQDGRTETLTMPSEDAQVAVYRAALAAAGVQPETVGVVEAHGTGTPIGDPIEYRSLARVYGAGTPCALGSAKSNMGHSTASAGTVGLIKAILSLRHGVVPPLLHFNRLPDELSDVETGLFVPQAVTPWPNGNDHTPKRVAVSSFGMSGTNVHAIVEEAPAEASAPESSPGDAEVGPRLFMLSSTSSDALRQTARQLATWVEEHQDCVAASDLAYTLARGRAHRPVRTAVVAANLPELVEGLREVADGDALYDAAVGHGDRGPVWVFSGQGSQWAAMGTQLLASEPVFAATIAKLEPVIAAESGFSVTEAITAQQTVTGIDKVQPAVFAVQVALAATMEQTYGVRPGAVVGHSMGESAAAVVAGALSLEDAARVICRRSKLMTRIAGAGAMGSVELPAKQVNSELMARGIDDVVVSVVASPQSTVIGGTSDTVRDLIARWEQRDVMAREVAVDVASHSPQVDPILDDLAAALADIAPMTPKVPYYSATLFDPREQPVCDGAYWVDNLRNTVQFAAAVQAAMEDGYRVFAELSPHPLLTHAVEQTGRSLDMSVAALAGMRREQPLPHGLRGLLTELHRAGAALDYSALYPAGRLVDAPLPAWTHARLFIDDDGQEQRAQGACTITVHPLLGSHVRLTEEPERHVWQGDVGTSVLSWLSDHQVHNVAALPGAAYCEMALAAAAEVFGEAAEVRDITFEQMLLLDEQTPIDAVASIDAPGVVNFTVETNRDGETTRHATAALRAAEDDCPPPGYDITALLQAHPHAVNGTAMRESFAERGVTLGAAFGGLTTAHTAEAGAATVLAEVALPASIRFQQGAYRIHPALLDACFQSVGAGVQAGTATGGLLLPLGVRSLRAYGPTRNARYCYTRLTKAFNDGTRGGEADLDVLDEHGTVLLAVRGLRMGTGTSERDERDRLVSERLLTLGWQQRALPEVGDGEAGSWLLIDTSNAVDTPDMLASTLTDALKSHGPQGTECASLSWSVQDTPPNDQAGLEKLGSQLRGRDGVVIVYGPRVGDPDEHSLLAGREQVRHLVRITRELAEFEGELPRLFVVTRQAQIVKPHDSGERANLEQAGLRGLLRVISSEHPMLRTTLIDVDEHTDVERVAQQLLSGSEEDETAWRNGDWYVARLTPSPLGHEERRTAVLDPDHDGMRVQVRRPGDLQTLEFVASDRVPPGPGQIEVAVSMSSINFADVLIAFGRFPIIDDREPQLGMDFVGVVTAVGEGVTGHQVGDRVGGFSEGGCWRTFLTCDANLAVTLPPGLTDEQAITAATAHATAWYGLNDLAQIKAGDKVLIHSATGGVGQAAISIARAKGAEIFATAGNPAKRAMLRDMGVEHVYDSRSVEFAEQIRRDTDGYGVDIVLNSLTGAAQRAGLELLAFGGRFVEIGKADVYGNTRLGLFPFRRGLTFYYLDLALMSVTQPDRVRELLATVFKLTADGVLTAPQCTHYPLAEAADAIRAMSNAEHTGKLVLDVPRSGRRSVAVTPEQAPLYRRDGSYIITGGLGGLGLFFASKLAAAGCGRIVLTARSQPNPKARQTIEGLRAAGADIVVECGNIAEPDTADRLVSAATATGLPLRGVLHSAAVVEDATLTNITDELIDRDWSPKVFGSWNLHRATLGQPLDWFCLFSSGAALLGSPGQGAYAAANSWVDVFAHWRRAQGLPVSAIAWGAWGEVGRATFLAEGGEIMITPEEGAYAFETLVRHDRAYSGYIPILGAPWLADLVRRSPWGEMFASTGQRSRGPSKFRMELLSLPQDEWAGRLRRLLVEQASVILRRTIDADRSFIEYGLDSLGMLEMRTHVETETGIRLTPKVIATNNTARALAQYLADTLAEEQAAAPAAS"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3276379", "fmax": "3282715", "strand": "-", "sequence": "ATGGAATCACGTGTCACTCCCGTTGCGGTGATCGGGATGGGATGTCGGCTTCCTGGGGGGATCAACTCGCCCGACAAACTGTGGGAGTCGTTGCTGCGCGGTGATGACTTGGTCACCGAGATTCCGCCCGACCGCTGGGACGCCGACGACTATTACGACCCTGAGCCAGGGGTTCCCGGGCGGTCGGTGTCCCGGTGGGGTGGGTTCCTTGACGACGTCGCCGGTTTCGATGCTGAGTTCTTCGGGATTAGCGAGCGGGAAGCGACCTCGATCGATCCGCAGCAGCGGCTACTGCTGGAAACGTCGTGGGAGGCGATCGAGCATGCTGGTCTGGATCCGGCGTCGTTGGCCGGGTCCTCGACGGCCGTTTTTACTGGGCTGACCCACGAGGACTACCTGGTACTCACCACAACGGCGGGCGGTTTGGCCAGTCCATATGTGGTTACCGGCCTCAACAACAGTGTGGCGTCAGGGCGGATCGCGCACACATTGGGTCTACATGGTCCGGCGATGACGTTTGACACCGCGTGTTCTTCGGGTCTGATGGCGGTGCACCTGGCCTGCCGCAGCCTGCATGACGGCGAAGCTGACCTCGCTTTGGCGGGCGGTTGTGCGGTGCTGCTGGAGCCGCATGCCAGTGTGGCGGCGTCTGCGCAGGGCATGCTGTCGTCAACCGGTCGGTGCCATTCATTCGATGCTGACGCGGATGGGTTTGTGCGTTCCGAGGGCTGCGCGATGGTGTTGCTGAAGCGACTGCCGGATGCGCTGCGCGACGGTAATCGGATCTTCGCCGTGGTGCGTGGCACGGCCACCAATCAGGACGGCCGCACGGAGACGCTCACCATGCCGTCCGAGGACGCCCAGGTTGCCGTGTACCGTGCGGCGTTGGCGGCGGCGGGCGTGCAGCCCGAAACGGTCGGTGTGGTCGAGGCGCACGGCACCGGTACGCCAATCGGCGACCCGATTGAGTACCGCAGCCTGGCGCGGGTGTATGGCGCGGGCACCCCCTGCGCGCTTGGATCGGCCAAGAGCAACATGGGGCACAGCACGGCATCGGCGGGGACCGTCGGGCTGATCAAGGCAATTCTGTCACTGCGGCACGGGGTGGTGCCGCCGCTGCTGCATTTCAATCGGCTGCCCGATGAGCTTTCCGACGTCGAGACCGGGCTCTTTGTGCCGCAAGCGGTTACGCCGTGGCCCAACGGTAATGATCACACACCGAAGCGGGTCGCGGTGTCCTCGTTCGGGATGTCCGGGACCAACGTGCATGCCATCGTGGAAGAGGCCCCAGCAGAAGCTTCCGCACCCGAGAGTTCACCGGGCGACGCTGAGGTGGGCCCGCGGCTATTCATGCTGTCGTCCACGTCCAGCGACGCACTGCGCCAGACGGCCCGCCAACTAGCCACCTGGGTGGAAGAACACCAGGACTGCGTGGCGGCCTCGGATCTGGCCTACACGCTGGCGCGTGGCCGCGCGCACCGGCCGGTGCGCACCGCGGTGGTTGCCGCCAACCTGCCGGAGCTCGTCGAGGGTTTGCGCGAGGTGGCCGACGGTGACGCCCTCTATGACGCGGCGGTGGGACACGGTGATCGAGGACCGGTCTGGGTCTTCTCCGGGCAAGGGTCGCAGTGGGCGGCGATGGGCACGCAATTGCTCGCCAGCGAACCAGTGTTCGCGGCCACCATCGCCAAGCTGGAGCCGGTGATCGCCGCAGAATCGGGATTCTCGGTGACCGAGGCGATAACGGCGCAGCAGACCGTGACCGGAATCGACAAAGTGCAGCCGGCAGTGTTCGCCGTTCAGGTCGCGTTGGCCGCCACCATGGAGCAAACCTACGGAGTGCGGCCGGGCGCGGTCGTCGGACACTCGATGGGTGAGTCGGCCGCGGCCGTCGTCGCGGGGGCACTGTCGCTCGAGGACGCGGCGCGCGTCATTTGCCGCCGCTCGAAGCTGATGACCCGCATAGCCGGTGCTGGTGCCATGGGCTCGGTGGAATTGCCCGCCAAGCAAGTGAATTCGGAGCTGATGGCACGCGGAATCGACGATGTTGTGGTCTCGGTGGTGGCGTCCCCGCAATCCACGGTGATCGGCGGTACGAGCGACACCGTTCGTGACCTCATCGCCCGTTGGGAGCAGCGGGACGTGATGGCGCGCGAGGTGGCCGTCGACGTGGCGTCGCACTCGCCTCAAGTCGATCCGATACTCGACGATTTGGCCGCGGCGCTGGCGGACATTGCTCCGATGACGCCCAAGGTGCCGTACTACTCGGCGACCCTGTTCGACCCGCGCGAGCAGCCGGTGTGCGATGGCGCTTACTGGGTGGACAATCTGCGCAACACGGTGCAGTTCGCCGCGGCGGTGCAGGCTGCGATGGAGGACGGCTACCGGGTCTTCGCGGAGCTGTCGCCCCACCCGCTGCTTACCCACGCCGTCGAACAGACGGGCCGAAGCCTCGACATGTCGGTCGCCGCCCTGGCCGGCATGCGGCGAGAGCAGCCTCTGCCGCATGGTCTGCGCGGCTTGCTGACGGAGCTGCACCGCGCGGGCGCCGCTTTGGACTATTCGGCGCTGTATCCCGCTGGGCGGCTGGTGGATGCGCCGCTGCCGGCGTGGACCCACGCCCGCCTATTCATCGACGATGATGGGCAAGAACAGCGGGCACAAGGTGCCTGCACCATCACCGTGCATCCGTTGCTTGGCTCGCATGTGCGGCTGACTGAGGAACCTGAGCGCCACGTCTGGCAGGGCGACGTTGGCACCTCGGTGCTGTCCTGGCTCAGCGATCATCAGGTGCATAACGTTGCCGCCCTTCCCGGCGCCGCCTACTGCGAGATGGCTTTGGCTGCGGCCGCTGAGGTCTTCGGCGAAGCGGCTGAGGTTCGCGACATCACCTTTGAGCAGATGTTGTTGCTCGACGAGCAGACCCCGATCGACGCCGTCGCATCGATCGACGCGCCTGGTGTCGTCAACTTCACCGTGGAGACCAACCGGGACGGTGAAACCACCCGGCATGCCACCGCGGCGCTGCGCGCCGCCGAAGATGACTGCCCGCCGCCGGGGTACGACATCACCGCTCTGCTGCAGGCGCATCCGCACGCCGTGAACGGGACCGCCATGCGGGAATCGTTCGCCGAGCGTGGTGTTACTTTGGGCGCCGCGTTCGGTGGTCTGACCACCGCGCATACCGCCGAGGCGGGAGCCGCGACGGTGCTGGCCGAGGTCGCGCTGCCCGCGTCGATCCGGTTCCAGCAGGGCGCCTACCGAATCCACCCGGCGCTGCTGGACGCTTGTTTCCAGTCGGTCGGCGCGGGCGTCCAGGCCGGTACGGCCACTGGTGGCCTGCTGTTGCCGTTGGGTGTGCGCAGCCTGCGTGCCTACGGGCCTACCCGCAATGCCCGCTACTGCTACACGCGGTTGACCAAGGCCTTCAACGACGGGACCCGAGGTGGTGAGGCCGACCTCGACGTGCTGGACGAGCACGGGACCGTCCTGTTGGCCGTGCGTGGGCTACGCATGGGAACCGGGACCTCCGAACGCGACGAGCGTGACCGCCTAGTCAGCGAGCGGCTACTGACCCTCGGATGGCAGCAGCGAGCGCTGCCCGAGGTTGGCGACGGCGAGGCTGGATCGTGGCTATTGATCGACACTTCCAACGCCGTCGACACCCCCGACATGTTGGCTTCCACGTTGACGGACGCGCTGAAGTCCCACGGCCCCCAAGGCACCGAATGCGCCAGCCTGTCCTGGTCGGTCCAGGACACCCCGCCCAACGATCAAGCTGGCCTCGAAAAGCTGGGCAGCCAGCTGCGTGGCCGCGATGGTGTGGTGATCGTGTATGGGCCTCGCGTCGGCGACCCCGATGAGCACAGTCTGCTGGCCGGTCGTGAACAGGTCCGTCACCTGGTTCGGATCACCCGGGAACTGGCTGAATTCGAGGGCGAGCTGCCGCGCTTGTTCGTGGTGACCAGACAAGCCCAGATAGTGAAGCCGCACGACTCGGGAGAAAGAGCCAACCTGGAGCAGGCCGGCCTGCGTGGTCTGCTACGGGTGATCAGCAGTGAACATCCGATGCTGCGCACCACCTTGATCGATGTGGACGAACACACGGACGTTGAGCGGGTGGCCCAGCAGCTGCTGAGCGGATCGGAAGAGGACGAGACGGCCTGGCGGAATGGCGACTGGTATGTGGCCCGCTTGACCCCCAGTCCGCTGGGCCATGAAGAGCGGCGCACCGCGGTCTTGGATCCCGACCACGACGGTATGCGGGTGCAGGTCCGCAGGCCGGGAGACTTGCAAACGTTGGAATTCGTTGCGAGTGACCGAGTTCCGCCCGGCCCCGGGCAAATCGAAGTCGCGGTCAGCATGTCCAGCATCAACTTCGCCGACGTTTTGATCGCGTTTGGACGATTCCCCATTATCGATGACCGCGAGCCGCAGTTGGGTATGGATTTCGTCGGTGTGGTGACTGCGGTCGGGGAAGGTGTCACCGGTCACCAGGTCGGTGATCGTGTTGGCGGTTTCTCCGAAGGTGGCTGTTGGCGGACGTTCCTCACCTGTGACGCCAACCTCGCGGTCACGCTGCCGCCCGGCTTGACCGATGAGCAGGCGATCACGGCGGCCACCGCGCATGCCACCGCCTGGTATGGGCTCAACGACCTGGCTCAGATCAAGGCCGGTGACAAAGTGTTGATTCACTCCGCCACCGGCGGTGTGGGGCAGGCGGCCATATCGATTGCCCGCGCCAAGGGAGCGGAGATTTTCGCGACCGCCGGCAATCCCGCGAAGCGAGCCATGCTGCGCGACATGGGCGTCGAGCATGTCTACGATTCGCGCAGCGTCGAGTTCGCCGAGCAGATCCGGCGCGACACCGACGGGTACGGCGTGGATATCGTGCTGAACTCGCTGACCGGCGCCGCCCAACGTGCGGGGCTGGAGTTGTTGGCCTTCGGCGGACGCTTCGTCGAAATCGGCAAGGCCGACGTTTACGGCAACACCCGGCTGGGGCTGTTCCCGTTCCGTCGCGGACTGACCTTCTACTACTTGGACCTCGCGCTGATGTCGGTCACCCAGCCCGACCGGGTCCGTGAGTTGCTGGCCACGGTGTTCAAGCTCACCGCAGACGGGGTGCTGACCGCACCGCAATGCACTCATTACCCGTTGGCCGAGGCGGCCGACGCCATCCGGGCAATGAGCAACGCCGAGCACACCGGCAAACTCGTGCTCGACGTACCGCGTAGCGGCCGTAGAAGCGTGGCGGTCACCCCGGAGCAAGCTCCGCTGTACCGCCGCGACGGCTCCTACATCATCACCGGCGGCCTGGGTGGCCTCGGCCTGTTCTTCGCCTCGAAGCTGGCCGCGGCGGGCTGTGGCCGGATCGTGCTGACCGCACGTTCCCAGCCCAACCCCAAAGCGCGGCAGACCATCGAAGGCCTGCGCGCGGCTGGGGCCGACATCGTGGTGGAGTGTGGCAACATCGCCGAACCCGACACGGCGGACCGGCTGGTGAGTGCGGCGACCGCTACCGGGCTTCCGCTGCGCGGTGTGCTGCACTCGGCGGCGGTGGTCGAGGATGCCACGCTGACCAACATCACCGATGAGCTCATCGATCGCGACTGGTCGCCCAAGGTGTTCGGATCCTGGAACCTACACCGCGCCACCCTCGGTCAGCCGCTGGACTGGTTCTGCTTGTTCTCCTCGGGAGCGGCATTGCTCGGCTCGCCGGGTCAGGGCGCCTACGCGGCGGCCAACAGCTGGGTCGACGTCTTCGCGCACTGGCGCCGCGCCCAGGGCCTGCCGGTCAGCGCGATTGCGTGGGGTGCGTGGGGCGAGGTCGGCCGCGCCACGTTCTTGGCCGAGGGGGGCGAAATCATGATCACCCCGGAGGAAGGTGCGTATGCCTTCGAGACGCTCGTGCGCCACGACCGCGCCTACAGCGGTTACATTCCGATCCTCGGGGCGCCATGGCTGGCCGACCTTGTCCGACGCAGCCCGTGGGGTGAAATGTTCGCATCCACTGGGCAGCGGTCAAGGGGCCCAAGCAAATTCCGCATGGAGCTCCTTTCGCTGCCGCAAGATGAATGGGCCGGCCGGCTACGGCGTCTGCTGGTTGAGCAGGCCAGTGTGATCCTGCGTCGCACGATCGACGCTGACCGCTCATTCATCGAGTACGGCCTGGATTCGCTGGGCATGCTCGAGATGCGTACCCACGTTGAAACCGAGACCGGGATACGCCTGACCCCCAAGGTCATCGCCACAAACAACACCGCCCGCGCTTTGGCCCAGTACTTGGCGGACACGCTGGCCGAGGAGCAGGCGGCGGCACCGGCGGCATCATAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004978", "ARO_id": "43165", "ARO_name": "Mycobacterium tuberculosis mas mutations confer resistance to pyrazinamide", "CARD_short_name": "Mtub_mas_PZA", "ARO_description": "Mutations in mas that can contribute to or confer resistance to pyrazinamide.", "ARO_category": {"43068": {"category_aro_accession": "3004882", "category_aro_cvterm_id": "43068", "category_aro_name": "pyrazinamide resistant mas", "category_aro_description": "Mas is a multifunctional mycocerosic acid synthase membrane-associated mas. It catalyzes the elongation of N-fatty acyl-CoA with methylamalonyl-CoA as the elongating agent to form mycocerosyl fatty acids present in mycobacterium.", "category_aro_class_name": "AMR Gene Family"}, "39997": {"category_aro_accession": "3003413", "category_aro_cvterm_id": "39997", "category_aro_name": "pyrazinamide", "category_aro_description": "Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.", "category_aro_class_name": "Antibiotic"}, "45737": {"category_aro_accession": "3007155", "category_aro_cvterm_id": "45737", "category_aro_name": "pyrazine antibiotic", "category_aro_description": "A group of antibiotics derived from pyrazine.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3725": {"model_id": "3725", "model_name": "Mycobacterium tuberculosis furA mutations confer resistance to isoniazid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"12570": "A14V"}, "clinical": {"12570": "A14V"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "225"}}, "model_sequences": {"sequence": {"8817": {"protein_sequence": {"accession": "NP_216425.2", "sequence": "MSSIPDYAEQLRTADLRVTRPRVAVLEAVNAHPHADTETIFGAVRFALPDVSRQAVYDVLHALTAAGLVRKIQPSGSVARYESRVGDNHHHIVCRSCGVIADVDCAVGEAPCLTASDHNGFLLDEAEVIYWGLCPDCSISDTSRSHP"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "2156148", "fmax": "2156592", "strand": "-", "sequence": "GTGTCCTCTATACCGGACTACGCCGAACAGCTCCGGACGGCCGACCTGCGCGTGACCCGACCGCGCGTCGCCGTCCTGGAAGCAGTGAATGCGCATCCACACGCCGACACGGAAACGATTTTCGGTGCCGTGCGTTTTGCGCTGCCCGACGTATCCCGGCAAGCCGTGTACGACGTGCTGCATGCCCTGACCGCCGCGGGCTTGGTGCGAAAGATCCAACCCTCGGGCTCCGTCGCGCGCTACGAGTCCAGGGTCGGCGACAACCACCATCACATCGTCTGCCGGTCTTGCGGGGTTATCGCCGATGTCGACTGTGCTGTTGGCGAGGCACCCTGTCTGACGGCCTCGGACCATAACGGCTTCCTGTTGGACGAGGCGGAGGTCATCTACTGGGGTCTATGTCCTGATTGTTCGATATCCGACACTTCGCGATCACATCCGTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004923", "ARO_id": "43109", "ARO_name": "Mycobacterium tuberculosis furA mutations confer resistance to isoniazid", "CARD_short_name": "Mtub_furA_INH", "ARO_description": "Mutations that occur in furA that result in or contribute to antibiotic resistance to isoniazid.", "ARO_category": {"43083": {"category_aro_accession": "3004897", "category_aro_cvterm_id": "43083", "category_aro_name": "isoniazid resistant furA", "category_aro_description": "Transcriptional regulator furA, represses the transcription of the catalase-peroxidase gene katG and its own transcription by binding to the promoter region.", "category_aro_class_name": "AMR Gene Family"}, "36659": {"category_aro_accession": "3000520", "category_aro_cvterm_id": "36659", "category_aro_name": "isoniazid", "category_aro_description": "Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.", "category_aro_class_name": "Antibiotic"}, "45734": {"category_aro_accession": "3007152", "category_aro_cvterm_id": "45734", "category_aro_name": "isoniazid-like antibiotic", "category_aro_description": "A group of antibiotics containing isoniazid and its derivatives.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3705": {"model_id": "3705", "model_name": "Mycobacterium tuberculosis clpC1 with mutation conferring resistance to pyrazinamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"9636": "G258V"}, "clinical": {"9636": "G258V"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "1600"}}, "model_sequences": {"sequence": {"8823": {"protein_sequence": {"accession": "YP_177995.1", "sequence": "MFERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYQGKEAAEAGTGGRGGESGSPSTSLVLDQFGRNLTAAAMEGKLDPVIGREKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGEVPETLKDKQLYTLDLGSLVAGSRYRGDFEERLKKVLKEINTRGDIILFIDELHTLVGAGAAEGAIDAASILKPKLARGELQTIGATTLDEYRKYIEKDAALERRFQPVQVGEPTVEHTIEILKGLRDRYEAHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEAGARMRIRRMTAPPDLREFDEKIAEARREKESAIDAQDFEKAASLRDREKTLVAQRAEREKQWRSGDLDVVAEVDDEQIAEVLGNWTGIPVFKLTEAETTRLLRMEEELHKRIIGQEDAVKAVSKAIRRTRAGLKDPKRPSGSFIFAGPSGVGKTELSKALANFLFGDDDALIQIDMGEFHDRFTASRLFGAPPGYVGYEEGGQLTEKVRRKPFSVVLFDEIEKAHQEIYNSLLQVLEDGRLTDGQGRTVDFKNTVLIFTSNLGTSDISKPVGLGFSKGGGENDYERMKQKVNDELKKHFRPEFLNRIDDIIVFHQLTREEIIRMVDLMISRVAGQLKSKDMALVLTDAAKALLAKRGFDPVLGARPLRRTIQREIEDQLSEKILFEEVGPGQVVTVDVDNWDGEGPGEDAVFTFTGTRKPPAEPDLAKAGAHSAGGPEPAAR"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "4038157", "fmax": "4040704", "strand": "-", "sequence": "ATGTTCGAACGATTTACCGACCGTGCCCGCAGGGTCGTCGTCCTGGCTCAGGAAGAGGCCAGGATGCTCAACCACAACTACATCGGCACCGAGCACATTCTTTTAGGCCTGATCCATGAAGGGGAAGGCGTTGCCGCCAAGTCACTGGAGTCGTTGGGGATCTCGCTGGAAGGTGTGCGCAGTCAGGTCGAGGAGATCATCGGCCAGGGCCAGCAGGCGCCGTCTGGGCACATTCCGTTTACCCCCCGCGCCAAAAAGGTCCTCGAGCTGAGCTTGCGTGAAGCGCTGCAGCTTGGCCACAACTACATCGGGACCGAACACATTTTGCTGGGCCTCATCCGAGAGGGTGAAGGCGTGGCCGCCCAGGTGCTGGTCAAGCTGGGCGCCGAGCTGACCCGGGTGCGCCAGCAGGTGATCCAGCTGCTCTCCGGTTACCAAGGCAAGGAGGCCGCCGAAGCCGGCACCGGCGGCCGCGGGGGAGAGTCCGGCTCTCCGTCTACGTCCTTGGTGCTCGACCAGTTCGGCCGCAACCTCACGGCGGCGGCGATGGAAGGCAAACTGGACCCGGTCATCGGCCGCGAGAAGGAAATCGAGCGGGTCATGCAGGTGCTCTCTCGGCGCACCAAGAACAACCCGGTGCTGATCGGCGAGCCCGGCGTCGGCAAGACCGCGGTCGTCGAAGGACTGGCGCAGGCCATCGTGCACGGCGAGGTGCCCGAGACGCTCAAGGACAAGCAGCTCTACACGCTGGATCTGGGATCGCTGGTGGCGGGTAGCCGCTACCGCGGTGACTTCGAGGAACGCCTCAAGAAGGTGCTCAAGGAGATCAACACCCGCGGTGACATCATCCTGTTTATCGACGAGCTGCACACCTTGGTCGGTGCTGGAGCCGCCGAGGGCGCGATCGACGCCGCCTCGATCCTGAAACCGAAGCTCGCTCGCGGTGAACTGCAAACGATCGGCGCCACCACGCTCGACGAATACCGCAAGTACATCGAGAAGGACGCCGCGCTGGAGCGCCGCTTCCAGCCGGTGCAGGTGGGTGAGCCGACGGTGGAGCACACCATCGAGATCCTCAAGGGCCTGCGGGACCGGTACGAGGCGCACCACCGGGTGTCGATCACCGATGCGGCGATGGTGGCCGCCGCGACCCTGGCCGACCGCTACATCAACGACCGGTTCCTGCCCGACAAGGCGATCGACCTGATCGACGAGGCGGGTGCTCGGATGCGGATTCGTCGCATGACCGCACCGCCAGACCTACGCGAGTTCGATGAGAAGATCGCCGAGGCTCGTCGGGAGAAGGAATCGGCTATCGACGCCCAGGACTTCGAGAAGGCCGCCAGCCTGCGCGACCGGGAGAAGACACTGGTCGCACAGCGTGCTGAGCGCGAAAAGCAGTGGCGTTCAGGCGATCTTGACGTGGTCGCGGAGGTCGACGACGAGCAGATCGCCGAGGTGCTGGGCAACTGGACCGGTATCCCGGTGTTCAAGCTCACCGAGGCCGAGACCACCCGGCTGTTGCGGATGGAAGAAGAGCTGCACAAGCGGATCATCGGGCAAGAGGACGCCGTCAAGGCCGTTTCCAAGGCCATCCGGCGTACCCGGGCCGGGCTGAAAGACCCCAAGCGCCCGTCGGGCTCGTTCATCTTCGCCGGCCCGTCCGGTGTCGGTAAGACCGAACTGTCCAAGGCGCTGGCCAACTTCTTGTTCGGTGACGACGACGCGCTTATTCAGATTGACATGGGTGAATTCCACGACCGGTTCACCGCGTCGCGGCTATTCGGCGCGCCGCCCGGATACGTCGGCTACGAGGAGGGCGGCCAACTCACCGAGAAGGTGCGGCGCAAGCCGTTCTCGGTGGTGCTGTTCGACGAGATCGAGAAGGCGCATCAGGAGATCTACAACAGCCTGCTGCAGGTGCTCGAGGATGGCCGGCTCACCGACGGGCAGGGCCGCACGGTGGACTTCAAGAACACCGTGCTGATCTTTACGTCCAATCTGGGCACCTCCGACATCTCTAAGCCGGTCGGTCTGGGCTTTTCCAAGGGCGGCGGTGAGAACGACTACGAGCGGATGAAACAGAAGGTCAACGACGAGCTGAAGAAACACTTCCGCCCGGAGTTCCTCAACCGCATCGACGACATCATCGTCTTCCACCAGCTGACCCGCGAGGAGATCATCCGGATGGTCGACCTGATGATCAGCCGGGTCGCCGGCCAGCTCAAGAGCAAGGACATGGCGCTGGTGCTGACCGATGCGGCCAAGGCGCTGCTGGCCAAGCGTGGCTTCGACCCGGTGTTGGGGGCCCGCCCGTTGCGGCGCACCATCCAGCGTGAGATCGAAGATCAGCTCTCGGAGAAGATCCTCTTCGAGGAGGTCGGGCCGGGTCAGGTGGTCACCGTCGACGTGGACAACTGGGACGGTGAAGGTCCCGGCGAGGACGCGGTGTTCACCTTCACCGGTACCCGCAAGCCGCCGGCCGAGCCGGATCTGGCCAAGGCTGGAGCGCACAGCGCGGGCGGCCCGGAGCCGGCCGCGCGGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004957", "ARO_id": "43143", "ARO_name": "Mycobacterium tuberculosis clpC1 with mutation conferring resistance to pyrazinamide", "CARD_short_name": "Mtub_clpC1_PZA", "ARO_description": "Mutations that occur in clpC1 that result in or contribute to antibiotic resistance to pyrazinamide.", "ARO_category": {"43064": {"category_aro_accession": "3004878", "category_aro_cvterm_id": "43064", "category_aro_name": "pyrazinamide resistant clpC1", "category_aro_description": "clpC1 is a subunit of the clp protease that is ATP-dependent. It functions to direct the clp protease to specific substrates. In the presence of ATP it hydrolyses proteins and may be involved in the degradation of denatured proteins.", "category_aro_class_name": "AMR Gene Family"}, "39997": {"category_aro_accession": "3003413", "category_aro_cvterm_id": "39997", "category_aro_name": "pyrazinamide", "category_aro_description": "Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.", "category_aro_class_name": "Antibiotic"}, "45737": {"category_aro_accession": "3007155", "category_aro_cvterm_id": "45737", "category_aro_name": "pyrazine antibiotic", "category_aro_description": "A group of antibiotics derived from pyrazine.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "3739": {"model_id": "3739", "model_name": "Mycobacterium tuberculosis fabG1 mutation conferring resistance to ethionamide", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"41339": {"param_type": "snp in promoter region", "param_description": "A SNP in the promoter region of a gene which alters transcription of that gene, encoded as [wild-type][-][position][mutation], for example t-11c. Var represents any possible substitution. This is a pilot parameter in need of further documentation.", "param_type_id": "41339", "param_value": {"13397": "c-15t", "14764": "g-17t", "14766": "c-15t", "14768": "a-16g", "14770": "t-8c", "14772": "t-8g", "14774": "t-8a"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"14217": "L203L"}, "clinical": {"14217": "L203L"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "425"}}, "model_sequences": {"sequence": {"8814": {"protein_sequence": {"accession": "NP_215999.1", "sequence": "MTATATEGAKPPFVSRSVLVTGGNRGIGLAIAQRLAADGHKVAVTHRGSGAPKGLFGVECDVTDSDAVDRAFTAVEEHQGPVEVLVSNAGLSADAFLMRMTEEKFEKVINANLTGAFRVAQRASRSMQRNKFGRMIFIGSVSGSWGIGNQANYAASKAGVIGMARSIARELSKANVTANVVAPGYIDTDMTRALDERIQQGALQFIPAKRVGTPAEVAGVVSFLASEDASYISGAVIPVDGGMGMGH"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "1673439", "fmax": "1674183", "strand": "+", "sequence": "GTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCCCGTTCAGTCCTGGTTACCGGAGGAAACCGGGGGATCGGGCTGGCGATCGCACAGCGGCTGGCTGCCGACGGCCACAAGGTGGCCGTCACCCACCGTGGATCCGGAGCGCCAAAGGGGCTGTTTGGCGTCGAATGTGACGTCACCGACAGCGACGCCGTCGATCGCGCCTTCACGGCGGTAGAAGAGCACCAGGGTCCGGTCGAGGTGCTGGTGTCCAACGCCGGCCTATCCGCGGACGCATTCCTCATGCGGATGACCGAGGAAAAGTTCGAGAAGGTCATCAACGCCAACCTCACCGGGGCGTTCCGGGTGGCTCAACGGGCATCGCGCAGCATGCAGCGCAACAAATTCGGTCGAATGATATTCATAGGTTCGGTCTCCGGCAGCTGGGGCATCGGCAACCAGGCCAACTACGCAGCCTCCAAGGCCGGAGTGATTGGCATGGCCCGCTCGATCGCCCGCGAGCTGTCGAAGGCAAACGTGACCGCGAATGTGGTGGCCCCGGGCTACATCGACACCGATATGACCCGCGCGCTGGATGAGCGGATTCAGCAGGGGGCGCTGCAATTTATCCCAGCGAAGCGGGTCGGCACCCCCGCCGAGGTCGCCGGGGTGGTCAGCTTCCTGGCTTCCGAGGATGCGAGCTATATCTCCGGTGCGGTCATCCCGGTCGACGGCGGCATGGGTATGGGCCACTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3004933", "ARO_id": "43119", "ARO_name": "Mycobacterium tuberculosis fabG1 mutation conferring resistance to ethionamide", "CARD_short_name": "Mtub_fabG1_ETO", "ARO_description": "Mutations that occur in Mycobacterium tuberculosis fabG1 resulting in or contributing to resistance in ethionamide.", "ARO_category": {"43074": {"category_aro_accession": "3004888", "category_aro_cvterm_id": "43074", "category_aro_name": "ethionamide resistant fabG1", "category_aro_description": "fabG1 is involved in the fatty acid synthesis pathway, acting in the first reduction step for mycolic acid. It is associated with ethionamide resistance.", "category_aro_class_name": "AMR Gene Family"}, "40067": {"category_aro_accession": "3003474", "category_aro_cvterm_id": "40067", "category_aro_name": "ethionamide", "category_aro_description": "Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.", "category_aro_class_name": "Antibiotic"}, "45738": {"category_aro_accession": "3007156", "category_aro_cvterm_id": "45738", "category_aro_name": "thioamide antibiotic", "category_aro_description": "A group of antibiotics possessing the thioamide functional group.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6065": {"model_id": "6065", "model_name": "VRA-F", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"13250": "K84E"}, "clinical": {"13250": "K84E"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"8888": {"protein_sequence": {"accession": "WP_323056190.1", "sequence": "MAILEVKQLTKIYGTKKMAQEVLRDINMSIEEGEFIAIMGPSGSGKTTLLNVLSSIDYISQGSITLKGKKLEKLSNKELSDIREHDIGFIFQEYNLLHTLTVKENIMLPLTVQKLDKEHMLNRYEKVAEALNILDISDKYPSELSGGQRQRTSAARAFITLPSIIFADEPTGALDSKSTQDLLKRLTRMNEAFKSTIIMVTHDPVAASYANRVVMLKDGQIFTELYQGDDDKHTFFKEIIRVQSVLGGVNYDL"}, "dna_sequence": {"accession": "NZ_JAYEPV010000001.1", "fmin": "691066", "fmax": "691828", "strand": "-", "sequence": "GTGGCAATTTTAGAAGTAAAACAATTAACAAAAATATATGGAACTAAAAAAATGGCACAAGAAGTGTTGCGAGATATCAATATGTCTATTGAAGAAGGCGAGTTTATTGCTATTATGGGTCCCTCTGGATCTGGGAAAACGACATTATTAAATGTTTTAAGTTCAATTGATTATATTTCACAAGGTTCTATTACATTAAAAGGAAAAAAATTAGAAAAGCTTTCAAACAAGGAATTATCTGATATACGCGAGCATGATATTGGTTTTATTTTTCAAGAGTATAATTTACTGCATACATTGACTGTTAAAGAAAACATAATGTTACCACTAACGGTTCAGAAGTTAGATAAAGAACATATGTTAAATCGTTATGAAAAAGTAGCAGAAGCATTAAATATATTGGATATTAGTGATAAATACCCTTCTGAATTGTCTGGTGGACAAAGACAACGAACATCTGCTGCAAGAGCGTTTATTACATTACCTTCTATTATATTTGCTGACGAACCAACAGGTGCACTGGATTCTAAAAGTACTCAAGATTTATTAAAACGATTAACAAGAATGAATGAAGCATTTAAGTCTACAATTATTATGGTAACGCATGATCCTGTTGCAGCAAGTTATGCCAATCGAGTAGTGATGCTAAAAGATGGTCAAATTTTCACTGAATTATACCAAGGGGATGACGATAAACATACCTTTTTCAAAGAAATAATACGTGTACAAAGTGTTTTAGGTGGCGTTAATTATGACCTTTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35508", "NCBI_taxonomy_name": "Staphylococcus aureus", "NCBI_taxonomy_id": "1280"}}}}, "ARO_accession": "3007843", "ARO_id": "46632", "ARO_name": "VRA-F", "CARD_short_name": "VRA-F", "ARO_description": "VRA-F is an ABC transporter ATP-binding protein, or ATP-binding cassette.", "ARO_category": {"36002": {"category_aro_accession": "0010001", "category_aro_cvterm_id": "36002", "category_aro_name": "ATP-binding cassette (ABC) antibiotic efflux pump", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes.", "category_aro_class_name": "AMR Gene Family"}, "35947": {"category_aro_accession": "0000028", "category_aro_cvterm_id": "35947", "category_aro_name": "vancomycin", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.", "category_aro_class_name": "Antibiotic"}, "36220": {"category_aro_accession": "3000081", "category_aro_cvterm_id": "36220", "category_aro_name": "glycopeptide antibiotic", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.", "category_aro_class_name": "Drug Class"}, "36298": {"category_aro_accession": "3000159", "category_aro_cvterm_id": "36298", "category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance.", "category_aro_class_name": "Efflux Component"}, "36001": {"category_aro_accession": "0010000", "category_aro_cvterm_id": "36001", "category_aro_name": "antibiotic efflux", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell.", "category_aro_class_name": "Resistance Mechanism"}}}, "6067": {"model_id": "6067", "model_name": "SIE-1", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "550"}}, "model_sequences": {"sequence": {"8890": {"protein_sequence": {"accession": "APL95059.1", "sequence": "MIATMTIAASLAISPAAAATGPEPEAMAAMDRAGGARASDDPLTRPMAVERAKEWLAPLPPERVFGNSYLVGFAGLSVALIDTGAGLVLIDGALPQAAPMILSNVRKLGFDPRDIKFILSTEPHYDHAGGIAALARDTGATVVASRRGAEGLRAGAHAKDDPQFDYGGAWPAVSRLRVMKDGEVLRIGRASITAHATPGHTMGSMTWSWNACEGKRCKAIVFASSLNPVSADRYRFTAPSSAPIVKGFEASYRRMGALKCDILISAHPDNAGAGRYGSGSGACRSYAERSRRLLAKRLAEERRETSK"}, "dna_sequence": {"accession": "CP013070.1", "fmin": "2379245", "fmax": "2380169", "strand": "-", "sequence": "ATGATCGCAACGATGACAATCGCCGCGTCGCTGGCCATCAGCCCGGCGGCGGCAGCGACAGGGCCGGAGCCGGAAGCCATGGCGGCCATGGACCGGGCGGGCGGCGCCCGCGCCTCCGATGACCCTCTGACCCGGCCGATGGCGGTCGAAAGAGCCAAGGAATGGCTTGCGCCCCTGCCGCCCGAAAGGGTTTTCGGCAACAGCTATCTGGTCGGCTTCGCGGGTCTCAGCGTCGCCTTGATCGACACGGGTGCGGGCCTGGTGCTGATCGACGGCGCGCTTCCGCAGGCGGCGCCGATGATCCTCAGCAATGTTCGCAAGCTGGGCTTCGACCCCAGAGACATCAAATTTATTCTGAGTACCGAGCCGCATTATGATCATGCTGGCGGGATCGCCGCCCTGGCGCGCGACACCGGCGCCACCGTGGTGGCCAGCCGGCGCGGCGCGGAGGGCCTGCGGGCAGGCGCGCATGCGAAGGACGATCCGCAATTCGACTATGGCGGCGCCTGGCCGGCGGTGTCGCGGCTGCGCGTCATGAAGGACGGAGAGGTTCTGAGGATCGGCCGCGCATCCATCACCGCGCATGCGACGCCGGGCCACACGATGGGCAGCATGACATGGAGCTGGAACGCCTGCGAGGGCAAGAGGTGCAAGGCGATCGTCTTCGCCTCCAGCCTCAATCCGGTGTCGGCCGACCGTTACCGTTTCACCGCGCCTTCCAGCGCGCCGATCGTCAAGGGCTTCGAAGCCAGCTACAGGCGCATGGGCGCTTTGAAGTGCGACATTTTGATCTCCGCGCATCCCGACAATGCGGGCGCGGGGCGGTATGGCAGTGGATCCGGGGCCTGCCGGTCCTATGCGGAACGTTCGCGCCGCCTGCTCGCGAAGCGGTTGGCCGAGGAGCGGCGAGAGACGTCGAAATAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "46636", "NCBI_taxonomy_name": "Sphingobium indicum B90A", "NCBI_taxonomy_id": "861109"}}}}, "ARO_accession": "3007846", "ARO_id": "46635", "ARO_name": "SIE-1", "CARD_short_name": "SIE-1", "ARO_description": "SIE-1 is SIE beta-lactamase gene family variant.", "ARO_category": {"46634": {"category_aro_accession": "3007845", "category_aro_cvterm_id": "46634", "category_aro_name": "SIE beta-lactamase", "category_aro_description": "SIE is a subclass B3 metallo-beta-lactamase with enzymatic activity against cephalosporins and carbapanems, first identified from Sphingobium indicum.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6000": {"model_id": "6000", "model_name": "Mycobacterium tuberculosis ddn mutation conferring resistance to nitroimidazole antibiotics", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"15418": "M1Var", "15420": "L49P"}, "clinical": {"15418": "M1Var", "15420": "L49P"}}, "40394": {"param_type": "nonsense mutation", "param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a stop codon, encoded as [wild type amino acid][position][Ter], for example Q42Ter.", "param_type_id": "40394", "param_value": {"15419": "W20Ter", "15423": "W88Ter", "15424": "W139Ter", "13131": "W20Ter"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "275"}}, "model_sequences": {"sequence": {"8721": {"protein_sequence": {"accession": "NP_218064.1", "sequence": "MPKSPPRFLNSPLSDFFIKWMSRINTWMYRRNDGEGLGGTFQKIPVALLTTTGRKTGQPRVNPLYFLRDGGRVIVAASKGGAEKNPMWYLNLKANPKVQVQIKKEVLDLTARDATDEERAEYWPQLVTMYPSYQDYQSWTDRTIPIVVCEP"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3986843", "fmax": "3987299", "strand": "+", "sequence": "ATGCCGAAATCACCGCCGCGGTTTCTGAATTCGCCGCTCAGCGACTTCTTTATCAAGTGGATGTCACGGATTAATACCTGGATGTACCGCCGCAACGACGGGGAGGGTCTGGGCGGCACCTTCCAGAAGATTCCGGTCGCGCTGCTGACCACCACCGGCCGCAAGACCGGCCAGCCGCGGGTCAACCCGCTCTACTTCCTGCGCGACGGTGGGCGGGTCATTGTCGCGGCCTCCAAGGGCGGCGCGGAGAAGAACCCGATGTGGTACCTCAACCTCAAGGCCAACCCCAAGGTTCAGGTACAGATCAAAAAGGAAGTGCTGGACCTTACCGCGCGGGACGCGACCGACGAGGAGCGCGCCGAATATTGGCCACAGTTGGTCACGATGTACCCAAGTTATCAGGACTACCAGTCCTGGACCGACCGCACGATCCCGATCGTGGTTTGCGAACCCTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3007661", "ARO_id": "46441", "ARO_name": "Mycobacterium tuberculosis ddn mutation conferring resistance to nitroimidazole antibiotics", "CARD_short_name": "Mtub_ddn_MULT", "ARO_description": "ddn is a protein-coding gene involved in the bioreductive activation of bicyclic 4-nitroimidazole prodrugs such as PA-824 and delamanid developed for anti-tuberculosis therapy against both replicating and persistent bacteria.", "ARO_category": {"46434": {"category_aro_accession": "3007656", "category_aro_cvterm_id": "46434", "category_aro_name": "antibiotic resistant Mycobacterium tuberculosis nitroreductase", "category_aro_description": "Inactivation of the F420-dependent anti-oxidant mechanism that protects M.tuberculosis against oxidative stress and bactericidal agents plays a role in antibiotic resistance.", "category_aro_class_name": "AMR Gene Family"}, "41931": {"category_aro_accession": "3004490", "category_aro_cvterm_id": "41931", "category_aro_name": "delamanid", "category_aro_description": "A novel nitroimidazole antibiotic for treating Mycobacterium tuberculosis infection. Delamanid inhibits bacterial cell wall growth by mycolic acid synthesis disruption and is particularly effective in combination therapies against multidrug-resistant tuberculosis.", "category_aro_class_name": "Antibiotic"}, "46306": {"category_aro_accession": "3007535", "category_aro_cvterm_id": "46306", "category_aro_name": "pretomanid", "category_aro_description": "Pretomanid is an antibiotic medication used for the treatment of multi-drug-resistant tuberculosis affecting the lungs.", "category_aro_class_name": "Antibiotic"}, "41239": {"category_aro_accession": "3004115", "category_aro_cvterm_id": "41239", "category_aro_name": "nitroimidazole antibiotic", "category_aro_description": "Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6068": {"model_id": "6068", "model_name": "NWM-1", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "550"}}, "model_sequences": {"sequence": {"8891": {"protein_sequence": {"accession": "QXM27671.1", "sequence": "MEPALFDRLTLAASVAALAGCSAGLASSESAAKIEDAQHSSDIVRFANECEDWDDWDKPAKPFQIHAKTYYVGTCGIAAILIEGEDGLVLIDTGTEPGSRQVEANIAALGHSVSDIDAILTSHEHFDHVGGLARLQALSGATVHTSAAALPVLRTGKDDPRDPQAGLHPPMAPVGGTIRALGDGEIVEIGGARIKALATPGHTLGAMSWEWESCDAAGCVTIVLADSLSAVSADGYKFNEHPEYVAMFRKGIARMAETTCDILLTPHPSASDMIARAKTGTFEGGMTCSEYADSKTKALDERLAKEAADE"}, "dna_sequence": {"accession": "MZ497415.1", "fmin": "0", "fmax": "933", "strand": "+", "sequence": "ATGGAGCCAGCTTTGTTCGATAGACTTACTCTTGCCGCCAGCGTCGCTGCGCTCGCCGGGTGCAGCGCCGGATTGGCATCCAGCGAAAGCGCCGCGAAGATCGAGGACGCGCAGCATTCGAGCGACATCGTCCGCTTCGCCAACGAATGCGAGGACTGGGACGATTGGGACAAGCCGGCCAAGCCCTTCCAGATCCATGCGAAGACCTATTACGTCGGCACCTGCGGGATTGCGGCGATCCTGATCGAGGGCGAGGATGGTCTGGTCCTGATCGACACGGGGACCGAGCCGGGGTCACGGCAGGTCGAGGCCAATATCGCCGCGTTGGGTCATTCCGTTTCCGACATCGATGCCATTCTCACTAGCCACGAGCACTTCGACCACGTCGGCGGTCTTGCGCGGCTGCAAGCGTTAAGCGGGGCGACGGTCCACACGAGCGCTGCCGCCCTGCCCGTTCTGCGCACCGGCAAGGACGACCCCCGCGATCCGCAGGCGGGGCTGCACCCTCCGATGGCTCCGGTCGGGGGAACGATACGCGCGCTGGGCGACGGCGAGATCGTGGAGATCGGCGGAGCGCGCATCAAGGCGCTGGCCACGCCGGGGCACACGCTCGGCGCGATGAGTTGGGAATGGGAAAGCTGCGACGCCGCAGGATGCGTTACCATCGTCCTTGCCGACAGCCTTTCCGCTGTCAGCGCGGACGGATACAAGTTCAACGAGCACCCCGAATACGTCGCCATGTTTCGCAAGGGCATCGCACGTATGGCGGAGACGACGTGCGACATCCTGCTGACCCCGCACCCTTCCGCCAGCGACATGATCGCGCGCGCCAAGACCGGCACTTTCGAAGGCGGCATGACCTGCTCCGAATATGCCGACAGCAAGACGAAAGCGCTGGACGAGCGGCTGGCCAAGGAAGCAGCGGACGAATGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36752", "NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287"}}}}, "ARO_accession": "3007848", "ARO_id": "46638", "ARO_name": "NWM-1", "CARD_short_name": "NWM-1", "ARO_description": "NWM-1 is a NWM beta-lactamase gene family variant.", "ARO_category": {"46637": {"category_aro_accession": "3007847", "category_aro_cvterm_id": "46637", "category_aro_name": "NWM beta-lactamase", "category_aro_description": "NWM is a subclass B3 metallo beta-lactamase with enzymatic activity against carbapenems, first identified in Pseudomonas aeruginosa.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6066": {"model_id": "6066", "model_name": "KPC-135", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"8889": {"protein_sequence": {"accession": "WP_262697131.1", "sequence": "MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"}, "dna_sequence": {"accession": "NG_088397.1", "fmin": "3", "fmax": "924", "strand": "+", "sequence": "ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35915", "NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573"}}}}, "ARO_accession": "3007844", "ARO_id": "46633", "ARO_name": "KPC-135", "CARD_short_name": "KPC-135", "ARO_description": "KPC-135 is a KPC-type class A beta-lactamase. KPC-125 is a variant of KPC-44, differing by a 6 basepair deletion.", "ARO_category": {"36198": {"category_aro_accession": "3000059", "category_aro_cvterm_id": "36198", "category_aro_name": "KPC beta-lactamase", "category_aro_description": "Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.", "category_aro_class_name": "AMR Gene Family"}, "35923": {"category_aro_accession": "0000004", "category_aro_cvterm_id": "35923", "category_aro_name": "monobactam", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6070": {"model_id": "6070", "model_name": "Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to clofazimine", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"40394": {"param_type": "nonsense mutation", "param_description": "A nucleotide substitution resulting in a change from an amino acid codon to a stop codon, encoded as [wild type amino acid][position][Ter], for example Q42Ter.", "param_type_id": "40394", "param_value": {"14546": "Q76Ter", "14584": "E113Ter", "14586": "Q115Ter", "14599": "E138Ter", "14605": "Y145Ter", "14612": "R156Ter", "14471": "Q22Ter", "14488": "R38Ter"}}, "snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"14478": "L32S", "14486": "A36V", "14496": "C46R", "14531": "I67S", "14536": "N70D", "14589": "L117R", "14592": "G121R", "14607": "M146T"}, "clinical": {"14478": "L32S", "14486": "A36V", "14496": "C46R", "14531": "I67S", "14536": "N70D", "14589": "L117R", "14592": "G121R", "14607": "M146T"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "300"}}, "model_sequences": {"sequence": {"8893": {"protein_sequence": {"accession": "NP_215192.1", "sequence": "MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "778989", "fmax": "779487", "strand": "+", "sequence": "GTGAGCGTCAACGACGGGGTCGATCAGATGGGCGCCGAGCCCGACATCATGGAATTCGTCGAACAGATGGGCGGCTATTTCGAGTCCAGGAGTTTGACTCGGTTGGCGGGTCGATTGTTGGGCTGGCTGCTGGTGTGTGATCCCGAGCGGCAGTCCTCGGAGGAACTGGCGACGGCGCTGGCGGCCAGCAGCGGGGGGATCAGCACCAATGCCCGGATGCTGATCCAATTTGGGTTCATTGAGCGGCTCGCGGTCGCCGGGGATCGGCGCACCTATTTCCGGTTGCGGCCCAACGCTTTCGCGGCTGGCGAGCGTGAACGCATCCGGGCAATGGCCGAACTGCAGGACCTGGCTGACGTGGGGCTGAGGGCGCTGGGCGACGCCCCGCCGCAGCGAAGCCGACGGCTGCGGGAGATGCGGGATCTGTTGGCATATATGGAGAACGTCGTCTCCGACGCCCTGGGGCGATACAGCCAGCGAACCGGAGAGGACGACTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3007852", "ARO_id": "46642", "ARO_name": "Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to clofazimine", "CARD_short_name": "Mtub_Rv0678_CFZ", "ARO_description": "Genetic variants of the transcription factor Rv0678, which regulates expression of the mmpS5/L5 efflux pump, that are associated with resistance to clofazimine antibiotics.", "ARO_category": {"46643": {"category_aro_accession": "3007853", "category_aro_cvterm_id": "46643", "category_aro_name": "clofazimine resistant Rv0678", "category_aro_description": "Loss-of-function mutations in the Mycobacterium Rv0678 gene associated with clofazimine resistance.", "category_aro_class_name": "AMR Gene Family"}, "40939": {"category_aro_accession": "3004012", "category_aro_cvterm_id": "40939", "category_aro_name": "clofazimine", "category_aro_description": "Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.", "category_aro_class_name": "Antibiotic"}, "35920": {"category_aro_accession": "0000001", "category_aro_cvterm_id": "35920", "category_aro_name": "fluoroquinolone antibiotic", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6071": {"model_id": "6071", "model_name": "Mycobacterium tuberculosis atpE with mutation conferring resistance to bedaquiline", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.", "model_param": {"snp": {"param_type": "single resistance variant", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with format [wild-type][position][mutation], e.g. R184Q. Var represents any possible substitution.", "param_type_id": "36301", "param_value": {"14624": "D28G", "14625": "D28A", "14626": "D28V", "14627": "E61D", "14628": "A63P", "14629": "I66M"}, "clinical": {"14624": "D28G", "14625": "D28A", "14626": "D28V", "14627": "E61D", "14628": "A63P", "14629": "I66M"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "100"}}, "model_sequences": {"sequence": {"8894": {"protein_sequence": {"accession": "NP_215821.1", "sequence": "MDPTIAAGALIGGGLIMAGGAIGAGIGDGVAGNALISGVARQPEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPVK"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "1461044", "fmax": "1461290", "strand": "+", "sequence": "ATGGACCCCACTATCGCTGCCGGCGCCCTCATCGGCGGTGGACTGATCATGGCCGGTGGCGCCATCGGCGCCGGTATCGGTGACGGTGTCGCCGGTAACGCGCTTATCTCCGGTGTCGCCCGGCAACCCGAGGCGCAAGGGCGGCTGTTCACACCGTTCTTCATCACCGTCGGTTTGGTTGAGGCGGCATACTTCATCAACCTGGCGTTTATGGCGCTGTTCGTCTTCGCTACACCCGTCAAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3007854", "ARO_id": "46644", "ARO_name": "Mycobacterium tuberculosis atpE with mutation conferring resistance to bedaquiline", "CARD_short_name": "Mtub_atpE_BDQ", "ARO_description": "Genetic variants of ATPase subunit C atpE with mutations associated with resistance to bedaquiline antibiotics.", "ARO_category": {"46244": {"category_aro_accession": "3007477", "category_aro_cvterm_id": "46244", "category_aro_name": "antibiotic resistant ATP synthase", "category_aro_description": "ATP synthase enzymes, specifically subunit C, resistant to diarylquinolone antibiotics including Bedaquiline. Mutations in ATP synthase confer antibiotic resistance by disrupting binding and blocking of ATP synthase reactions by Bedaquiline.", "category_aro_class_name": "AMR Gene Family"}, "41933": {"category_aro_accession": "3004492", "category_aro_cvterm_id": "41933", "category_aro_name": "bedaquiline", "category_aro_description": "A diarylquinoline antibiotic drug sold under the brand name Sirturo, used to treat infection from Mycobacterium spp., particularly multidrug-resistant tuberculosis. Bedaquiline disrupts ATP synthase by proton pump blockage, inhibiting ATP synthesis.", "category_aro_class_name": "Antibiotic"}, "41932": {"category_aro_accession": "3004491", "category_aro_cvterm_id": "41932", "category_aro_name": "diarylquinoline antibiotic", "category_aro_description": "A class of antibiotics used to treat specifically Mycobacterium tuberculosis infection; therefore, referred to as an antimycobacterial. Diarylquinoline antibiotics inhibit ATP synthesis in tuberculosis cells by disruption of mycobacterial ATP synthase.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6072": {"model_id": "6072", "model_name": "KPC-134", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "550"}}, "model_sequences": {"sequence": {"8895": {"protein_sequence": {"accession": "UVJ69199.1", "sequence": "MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARATSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDNRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"}, "dna_sequence": {"accession": "OP293349.1", "fmin": "5", "fmax": "911", "strand": "+", "sequence": "ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGCTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAACCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35915", "NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573"}}}}, "ARO_accession": "3007857", "ARO_id": "46647", "ARO_name": "KPC-134", "CARD_short_name": "KPC-134", "ARO_description": "KPC-134 is an inhibitor-resistant KPC-2 variant which confers resistance to ceftazidime-avibactam.", "ARO_category": {"36727": {"category_aro_accession": "3000588", "category_aro_cvterm_id": "36727", "category_aro_name": "avibactam", "category_aro_description": "Serine beta-lactamase inhibitor targeting class A, class C, and some class D enzymes.", "category_aro_class_name": "Adjuvant"}, "36198": {"category_aro_accession": "3000059", "category_aro_cvterm_id": "36198", "category_aro_name": "KPC beta-lactamase", "category_aro_description": "Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.", "category_aro_class_name": "AMR Gene Family"}, "35977": {"category_aro_accession": "0000060", "category_aro_cvterm_id": "35977", "category_aro_name": "ceftazidime", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.", "category_aro_class_name": "Antibiotic"}, "45634": {"category_aro_accession": "3007072", "category_aro_cvterm_id": "45634", "category_aro_name": "ceftazidime-avibactam", "category_aro_description": "An antibiotic-adjuvant admixture of the beta-lactam antibiotic ceftazidime and the non-beta-lactam beta-lactamase inhibitor avibactam.", "category_aro_class_name": "Antibiotic+Adjuvant"}, "35923": {"category_aro_accession": "0000004", "category_aro_cvterm_id": "35923", "category_aro_name": "monobactam", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6074": {"model_id": "6074", "model_name": "BIM-1", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"8897": {"protein_sequence": {"accession": "ANY85569.1", "sequence": "MRISLALCLLSILNFAVAEEVLPEIKVEKLEEGIYLHTSYLEYQGNIYEKHGLVVIDDRKAYIIDTPVLAIDTERLVKWFEERNFTIGASFSTHFHSDSSGGIEWLNKNSIPTYASELTNELLKKDGKAQAKNSFNAVSFWLVKNKIEVFYPGPGHTQDNEVVWIPSKKILFGGCFVKPDGLGYLGDANLEAWPNSARKLMSKYSNAKLVIPSHSEIGNASLLKRTWEQAVKGLNDSKKTSQLSK"}, "dna_sequence": {"accession": "CP016446.1", "fmin": "14508", "fmax": "15246", "strand": "-", "sequence": "ATGAGAATATCGTTAGCTTTATGCTTGCTTAGTATTTTAAATTTTGCTGTTGCAGAAGAGGTATTGCCAGAAATAAAAGTTGAAAAGCTAGAAGAAGGAATCTATCTTCACACATCTTATCTAGAGTATCAGGGAAATATTTATGAAAAACATGGGTTGGTAGTTATTGATGATCGTAAGGCATATATAATTGATACGCCAGTTTTGGCTATAGATACTGAGCGGCTAGTAAAGTGGTTTGAAGAGCGTAACTTTACTATAGGGGCTAGTTTCTCAACACATTTTCATAGTGACAGTTCCGGCGGCATAGAATGGCTAAATAAAAATTCTATTCCTACATATGCATCTGAATTAACAAATGAACTTCTAAAAAAAGACGGCAAGGCGCAAGCTAAAAACTCTTTTAATGCAGTTAGTTTTTGGCTAGTTAAAAACAAAATTGAAGTTTTTTATCCGGGGCCAGGGCATACACAGGATAACGAGGTCGTGTGGATACCTAGTAAGAAAATATTATTCGGTGGTTGTTTTGTTAAGCCAGACGGTCTTGGGTATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAATTCTGCTAGAAAGTTAATGTCTAAATATAGCAACGCAAAACTGGTTATTCCAAGCCATAGTGAAATAGGAAATGCATCACTCTTGAAGCGTACATGGGAGCAGGCTGTTAAAGGGCTAAATGACAGTAAAAAAACATCACAGCTCAGCAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36803", "NCBI_taxonomy_name": "Pseudomonas putida", "NCBI_taxonomy_id": "303"}}}}, "ARO_accession": "3007859", "ARO_id": "46649", "ARO_name": "BIM-1", "CARD_short_name": "BIM-1", "ARO_description": "BIM-1 is an ambler molecular class B beta-lactamase. It confers resistance to carbapenems and cephalosporins.", "ARO_category": {"46648": {"category_aro_accession": "3007858", "category_aro_cvterm_id": "46648", "category_aro_name": "BIM beta-lactamase", "category_aro_description": "BIM is a family of ambler molecular class B beta-lactamases from Pseudomonas putida. It confers resistance to carbapenems and cephalosporins.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6073": {"model_id": "6073", "model_name": "CHM-1", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "475"}}, "model_sequences": {"sequence": {"8896": {"protein_sequence": {"accession": "QAT79363.1", "sequence": "MKTTLTHIVAIVFSFVIISCGSQHKDHFKAKEVYTSPHLVITQISEHSFIHTSFKQTNDFGNVPCNGLVVKNNNETIVFDTPINDKSSEELIQWINGTLHAKINAVIPTHFHDDSSGGLQAFHNHHIPSYAYSKTIELAKENKFVIPENSFNDSLVLKVGNEKTITRFFGEGHTKDNVVGYFPGEHILFGGCLLKELDAGKGYLGDANVAAWSNTVEKVKKEYPDVKIVVPGHGEYGNGKLLDYTITLFKTQ"}, "dna_sequence": {"accession": "MK401906.1", "fmin": "0", "fmax": "759", "strand": "+", "sequence": "ATGAAAACTACCCTTACCCATATAGTCGCTATAGTATTTTCTTTCGTCATCATAAGCTGTGGCTCTCAACATAAAGACCATTTTAAAGCAAAAGAAGTGTATACATCTCCCCATCTGGTTATTACCCAGATTTCTGAACATTCTTTTATCCATACTTCTTTTAAACAAACAAATGATTTTGGTAATGTTCCCTGCAACGGACTTGTTGTAAAAAATAATAATGAAACCATTGTTTTCGACACCCCCATTAATGACAAAAGTTCAGAAGAACTGATACAATGGATCAATGGAACACTTCATGCAAAAATAAATGCCGTTATTCCGACCCATTTCCATGATGACAGTTCAGGAGGATTGCAGGCATTTCATAATCATCATATTCCTTCCTATGCCTATTCCAAAACCATTGAATTAGCCAAAGAAAACAAGTTTGTAATTCCTGAAAACAGTTTTAATGATTCGCTGGTTTTAAAAGTTGGCAATGAAAAAACTATCACGAGGTTTTTCGGTGAAGGTCATACCAAAGATAATGTGGTAGGGTATTTCCCTGGTGAACATATATTGTTTGGAGGCTGTTTATTAAAAGAGCTTGATGCAGGTAAAGGATATCTGGGAGATGCTAATGTGGCAGCATGGTCCAATACAGTTGAAAAAGTGAAAAAAGAATATCCTGATGTGAAAATTGTGGTTCCGGGACATGGAGAATATGGGAATGGAAAACTACTGGACTATACCATTACATTATTTAAAACTCAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "46236", "NCBI_taxonomy_name": "Chryseobacterium sp.", "NCBI_taxonomy_id": "1871047"}}}}, "ARO_accession": "3007855", "ARO_id": "46645", "ARO_name": "CHM-1", "CARD_short_name": "CHM-1", "ARO_description": "CHM is a subclass B1 metallo B-lactamase with enzymatic activity against cephalosporins and carbapenems, first identified in the Chryseobacterium spp. functional gene library.", "ARO_category": {"46646": {"category_aro_accession": "3007856", "category_aro_cvterm_id": "46646", "category_aro_name": "CHM beta-lactamase", "category_aro_description": "CHM is a subclass B1 metallo B-lactamase with enzymatic activity against cephalosporins and carbapenems, first identified in the Chryseobacterium spp. functional gene library.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "6075": {"model_id": "6075", "model_name": "DYB-1", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "475"}}, "model_sequences": {"sequence": {"8903": {"protein_sequence": {"accession": "BES62776.2", "sequence": "MLKKFLLMIQVFCVATISAQSKTEKTEIADDIEILKLSDNLYLHRSFLETQSWGKVGANGLILIKNNEALLIDTPWNNEQTERLDKWISNSLHATIKTVIPTHWHEDRMGGLAYLQSKGVKSYANEQTIELAKTKNLPIPDTGFKDSIDINFQGFDLKLYYPGGGHTTDNIIVWIPSEDILFGGCFIKDLQSSNLGNLADADVAAWPQSIKWVLTKFPDIKTVVPGHGNMGGYNLLTHTLKLINEHNTVR"}, "dna_sequence": {"accession": "AP028867.1", "fmin": "3823966", "fmax": "3824719", "strand": "-", "sequence": "ATGCTAAAAAAATTCCTACTCATGATACAGGTATTCTGTGTCGCAACAATCTCGGCTCAATCTAAAACTGAAAAAACCGAGATTGCAGATGATATCGAAATTCTGAAATTATCAGACAACCTTTACCTTCACAGAAGTTTTCTCGAAACCCAAAGCTGGGGTAAAGTAGGAGCAAACGGATTGATTCTCATAAAGAACAACGAAGCATTGCTTATTGATACTCCGTGGAACAATGAACAAACCGAAAGACTCGATAAATGGATATCAAACTCTTTACATGCAACCATTAAAACAGTAATACCTACCCATTGGCACGAAGACCGCATGGGCGGCTTAGCTTACCTTCAGTCGAAAGGAGTAAAATCTTATGCTAATGAGCAGACGATAGAACTAGCCAAAACTAAAAACCTTCCTATACCCGACACCGGATTTAAAGATTCAATCGACATCAATTTTCAGGGATTCGATCTCAAACTATATTATCCGGGAGGAGGACATACTACTGACAATATAATTGTATGGATTCCGTCCGAAGATATCCTTTTCGGAGGGTGTTTTATCAAGGACTTGCAATCATCCAATCTGGGAAATCTTGCCGATGCCGATGTTGCAGCATGGCCACAATCGATAAAATGGGTTCTAACCAAGTTTCCTGATATTAAGACTGTTGTTCCCGGACACGGTAACATGGGAGGATACAACCTCTTGACCCATACATTAAAGCTTATTAATGAACATAATACGGTCAGGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "46652", "NCBI_taxonomy_name": "Dysgonomonas capnocytophagoides", "NCBI_taxonomy_id": "45254"}}}}, "ARO_accession": "3007861", "ARO_id": "46651", "ARO_name": "DYB-1", "CARD_short_name": "DYB-1", "ARO_description": "DYB-1 is a subclass B1 metallo-beta-lactamases identified from Dysgonomonas capnocytophagoides. DYB-1 is associated with resistance to meropenem and ceftazidime.", "ARO_category": {"46650": {"category_aro_accession": "3007860", "category_aro_cvterm_id": "46650", "category_aro_name": "DYB beta-lactamase", "category_aro_description": "DYB is a family of subclass B1 metallo-beta-lactamases identified from Dysgonomonas capnocytophagoides. These enzymes confer resistance to beta-lactam antibiotics, including carbapenems.", "category_aro_class_name": "AMR Gene Family"}, "35977": {"category_aro_accession": "0000060", "category_aro_cvterm_id": "35977", "category_aro_name": "ceftazidime", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.", "category_aro_class_name": "Antibiotic"}, "35990": {"category_aro_accession": "0000073", "category_aro_cvterm_id": "35990", "category_aro_name": "meropenem", "category_aro_description": "Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.", "category_aro_class_name": "Antibiotic"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7301": {"model_id": "7301", "model_name": "ACT-100", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10128": {"protein_sequence": {"accession": "UHK14157.1", "sequence": "MKTKSLCCALMLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAKAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794654.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCAAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007883", "ARO_id": "46675", "ARO_name": "ACT-100", "CARD_short_name": "ACT-100", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-100.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7302": {"model_id": "7302", "model_name": "ACT-101", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10129": {"protein_sequence": {"accession": "UHK14158.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWIHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794655.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAGGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGATACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007884", "ARO_id": "46676", "ARO_name": "ACT-101", "CARD_short_name": "ACT-101", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-101.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7303": {"model_id": "7303", "model_name": "ACT-102", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10130": {"protein_sequence": {"accession": "UHK14159.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGHPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGATRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWVKANMNPDALPNSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAQTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794656.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCATCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCGCAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGAATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCCAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007885", "ARO_id": "46677", "ARO_name": "ACT-102", "CARD_short_name": "ACT-102", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-102.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7304": {"model_id": "7304", "model_name": "ACT-103", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10131": {"protein_sequence": {"accession": "UHK14163.1", "sequence": "MKTKSLFCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794660.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTTCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCTGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCTCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGTTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007886", "ARO_id": "46678", "ARO_name": "ACT-103", "CARD_short_name": "ACT-103", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-103.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7305": {"model_id": "7305", "model_name": "ACT-104", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10132": {"protein_sequence": {"accession": "UHK14164.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGHPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQDWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEDEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKKLGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794661.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCACCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAGGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCATCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAAGACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGACGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGAAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007887", "ARO_id": "46679", "ARO_name": "ACT-104", "CARD_short_name": "ACT-104", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-104.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7306": {"model_id": "7306", "model_name": "ACT-105", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10133": {"protein_sequence": {"accession": "UMO60338.1", "sequence": "MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIVRGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"}, "dna_sequence": {"accession": "OM575023.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGTTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTAACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTTGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCAGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36926", "NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645"}}}}, "ARO_accession": "3007888", "ARO_id": "46680", "ARO_name": "ACT-105", "CARD_short_name": "ACT-105", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-105.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7307": {"model_id": "7307", "model_name": "ACT-106", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10134": {"protein_sequence": {"accession": "ULU82602.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADAPLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKRIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "OM617739.1", "fmin": "0", "fmax": "1146", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCCCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCGGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGTTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36771", "NCBI_taxonomy_name": "Proteus mirabilis", "NCBI_taxonomy_id": "584"}}}}, "ARO_accession": "3007889", "ARO_id": "46681", "ARO_name": "ACT-106", "CARD_short_name": "ACT-106", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-106.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7308": {"model_id": "7308", "model_name": "ACT-107", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10135": {"protein_sequence": {"accession": "UNN26045.1", "sequence": "MIKKSLCCALLLGMSYSGFTAQLSEKQLAEAVERTVTPLMKAHAIPGMAVAVIYQGQPHCFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPATKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDTASLLRFYQTWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTERVFKPLKLNHTWINVPKSEAQHYAWGYREGKPVHVSPGMLDAEAYGVKTNVQDMAAWVMANMAPENVAEASLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTLVDGSDNNVALAPLPAREVSPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "OM967044.1", "fmin": "2", "fmax": "1148", "strand": "+", "sequence": "ATGATCAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATGTCATATTCCGGCTTTACCGCTCAGCTGTCAGAAAAACAGTTAGCTGAGGCGGTTGAACGTACCGTTACTCCGCTGATGAAGGCACACGCTATTCCGGGCATGGCGGTTGCCGTGATTTACCAGGGCCAGCCGCACTGTTTCACCTTCGGCAAAGCCGATGTCGCCGCGAATAAACCCGTCACGCCGCAAACCCTGTTCGAGCTGGGCTCCATCAGTAAAACGTTCACCGGCGTGCTGGGCGGTGATGCCATTGCCCGCGGCGAGATTTCGCTGGGCGATCCGGCAACGAAATACTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGCATTCGAATGCTGGATCTGGCGACCTACACTGCGGGAGGTCTGCCGCTGCAGGTACCTGATGACGTGACGGACACCGCGTCGCTTCTGCGCTTTTACCAGACCTGGCAGCCGCAGTGGAAACCGGGCACCACGCGACTGTATGCCAACGCCAGCATCGGCCTGTTTGGCGCGCTGGCGGTTAAGCCTTCCGGCATGAGCTTTGAGCAGGCCATGACGGAACGCGTCTTTAAACCATTGAAGCTGAATCATACCTGGATTAACGTCCCGAAAAGCGAAGCGCAGCACTACGCATGGGGCTACCGGGAGGGGAAACCGGTCCACGTCTCACCAGGAATGCTGGACGCCGAAGCCTACGGCGTGAAAACCAACGTGCAGGATATGGCAGCCTGGGTGATGGCCAACATGGCACCGGAGAACGTTGCTGAAGCGTCACTTAAACAAGGTATTGCGCTGGCGCAGTCGCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACGCTGGTCGATGGCAGTGATAATAACGTTGCGCTGGCGCCGCTGCCTGCGAGAGAAGTGAGCCCTCCAGCTCCACCGGTCAAAGCATCGTGGGTACACAAAACGGGTTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTCATCCCGGAGAAAGAGCTTGGCATCGTGATGCTGGCGAACAAGAGCTATCCGAACCCGGCGCGGGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47907", "NCBI_taxonomy_name": "Enterobacter huaxiensis", "NCBI_taxonomy_id": "2494702"}}}}, "ARO_accession": "3007890", "ARO_id": "46682", "ARO_name": "ACT-107", "CARD_short_name": "ACT-107", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-107.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7309": {"model_id": "7309", "model_name": "ACT-108", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10136": {"protein_sequence": {"accession": "UQM99653.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEVNTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQVGIVMLANKSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "OL445411.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGTCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGGTCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007891", "ARO_id": "46683", "ARO_name": "ACT-108", "CARD_short_name": "ACT-108", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-108.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7310": {"model_id": "7310", "model_name": "ACT-109", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10137": {"protein_sequence": {"accession": "UTT87806.1", "sequence": "MMKKSLCCALLLSTSCAALAAPMSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIIMLANKSYPNPERVEAAYRILSALQ"}, "dna_sequence": {"accession": "OP022995.1", "fmin": "0", "fmax": "1146", "strand": "-", "sequence": "ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTATGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATTTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCTGAAGCGTATGGCGTGAAAACCAACGTTAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGCGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAGAAGGAACTCGGCATCATTATGCTGGCGAACAAGAGCTATCCGAACCCGGAACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "45936", "NCBI_taxonomy_name": "Enterobacter ludwigii", "NCBI_taxonomy_id": "299767"}}}}, "ARO_accession": "3007892", "ARO_id": "46684", "ARO_name": "ACT-109", "CARD_short_name": "ACT-109", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-109.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7311": {"model_id": "7311", "model_name": "ACT-110", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10138": {"protein_sequence": {"accession": "BDT38917.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDIASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAFRILSALQ"}, "dna_sequence": {"accession": "LC733682.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCTGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATAGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATTCCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007893", "ARO_id": "46685", "ARO_name": "ACT-110", "CARD_short_name": "ACT-110", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-110.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7312": {"model_id": "7312", "model_name": "ACT-111", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10139": {"protein_sequence": {"accession": "RTM78732.1", "sequence": "MMKKTLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEITLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPKWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMMPDSLQDSPLKHGIALAQSRYWRVGAMYQGLGWEMLNWPVDAQTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "RXSJ01000003.1", "fmin": "17151", "fmax": "18297", "strand": "-", "sequence": "ATGATGAAAAAAACCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGCACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCTGATGTTGCAGCGAACAAACCCGTCACCCCGCAAACCTTGTTCGAGCTGGGTTCGATAAGTAAAACCTTCACCGGCGTATTGGGTGGTGATGCGATTGCGCGCGGTGAAATAACGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTGCAGGTGCCGGATGAGGTCACGGATACCGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCAAAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACACCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCCTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGATGCCGGACTCCCTTCAGGATTCCCCACTTAAACACGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGAGCCATGTATCAAGGATTGGGCTGGGAAATGCTGAACTGGCCGGTCGACGCCCAAACGGTAGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCAAGAGAAGTGAATCCACCGGCACCACCGGTTAAGGCCTCCTGGGTCCATAAAACGGGCTCTACCGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATACTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47909", "NCBI_taxonomy_name": "Enterobacter quasiroggenkampii", "NCBI_taxonomy_id": "2497436"}}}}, "ARO_accession": "3007894", "ARO_id": "46686", "ARO_name": "ACT-111", "CARD_short_name": "ACT-111", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-111.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7313": {"model_id": "7313", "model_name": "ACT-112", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10140": {"protein_sequence": {"accession": "WEG44939.1", "sequence": "MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEMSLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQYWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OQ592375.1", "fmin": "3", "fmax": "1149", "strand": "+", "sequence": "ATGATGAAAAAATCCCTGTGCTGCGCTCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGTAAGGCCGATGTCGCCGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATGTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTACTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGATGCCGAAGCATATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGGGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAAGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCACCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAGAAGGAACTCGGCATCGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "45936", "NCBI_taxonomy_name": "Enterobacter ludwigii", "NCBI_taxonomy_id": "299767"}}}}, "ARO_accession": "3007895", "ARO_id": "46687", "ARO_name": "ACT-112", "CARD_short_name": "ACT-112", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-112.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7314": {"model_id": "7314", "model_name": "ACT-113", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10141": {"protein_sequence": {"accession": "WEG44940.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALVVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLKWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "OQ592376.1", "fmin": "3", "fmax": "1149", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGTGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAAATGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007896", "ARO_id": "46688", "ARO_name": "ACT-113", "CARD_short_name": "ACT-113", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-113.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7315": {"model_id": "7315", "model_name": "ACT-115", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10142": {"protein_sequence": {"accession": "AXQ35263.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"}, "dna_sequence": {"accession": "CP031726.1", "fmin": "3150070", "fmax": "3151216", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCATTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007897", "ARO_id": "46689", "ARO_name": "ACT-115", "CARD_short_name": "ACT-115", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-115.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7316": {"model_id": "7316", "model_name": "ACT-116", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10143": {"protein_sequence": {"accession": "WEY36194.1", "sequence": "MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "OQ642076.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGAATGCTGGATCTGGCAACCTATACCGCAGGTGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACATGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTAATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCAAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007898", "ARO_id": "46690", "ARO_name": "ACT-116", "CARD_short_name": "ACT-116", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-116.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7317": {"model_id": "7317", "model_name": "ACT-117", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10144": {"protein_sequence": {"accession": "WEY36195.1", "sequence": "MMKKSLCCALLLSTSCAALAAPMSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKSEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGIQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OQ642077.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTATGTCAGAAACACAACTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCCGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACTTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTACGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACAGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGTCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGCATACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTGGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCGGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007899", "ARO_id": "46691", "ARO_name": "ACT-117", "CARD_short_name": "ACT-117", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-117.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7318": {"model_id": "7318", "model_name": "ACT-118", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10145": {"protein_sequence": {"accession": "WEY36196.1", "sequence": "MIKKSLCCALLLGVSCSSIAASMTEKQLADVVEKSITPLMKAQSIPGMAIAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAVARGEISLGDPVIKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDSASLQRFYQTWQPQWKPGTTRLYANASIGLFGALAVKPSGMGFEQAMTTRVFKPLGLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVVANMAPDNVQDASLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "OQ642078.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATCAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCGTGTCATGCTCCAGCATTGCTGCGTCGATGACAGAAAAACAGCTGGCTGACGTGGTGGAAAAAAGCATTACCCCCCTGATGAAAGCGCAGTCCATTCCGGGCATGGCGATTGCCGTGATCTACCAGGGCCAGCCGCACTATTTTACTTTTGGTAAAGCCGATGTTGCAGCGAACAAACCTGTTACCCCACAAACCCTGTTCGAACTAGGTTCTATCAGTAAAACTTTCACCGGCGTATTGGGCGGCGATGCTGTTGCCCGCGGTGAGATATCGCTGGGCGATCCGGTTATAAAGTACTGGCCTGAGCTGACGGGCAAGCAGTGGCAGGGGATTCGCATGCTGGATCTGGCGACCTATACCGCGGGAGGGTTACCGCTCCAGGTGCCGGATGAGGTGACAGACAGCGCGTCGCTGCAGCGCTTTTACCAGACATGGCAGCCGCAGTGGAAACCTGGCACCACGCGATTGTATGCGAACGCCAGCATCGGTCTGTTTGGCGCACTGGCGGTTAAACCTTCCGGCATGGGCTTTGAACAGGCCATGACGACGCGGGTCTTTAAACCGCTCGGGCTCGACCATACGTGGATCAACGTTCCGAAAGCAGAAGAGGCACATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTGTCACCGGGGATGCTGGATGCCGAAGCCTACGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGGTGGCCAATATGGCTCCGGATAACGTTCAGGACGCATCGCTGAAGCAAGGCATTACGCTGGCGCAGTCGCGCTACTGGCGCGTGGGGGCCATGTATCAGGGATTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAACAAGGTCGCGCTGGCCCCCCTGCCTGCGAGAGAAGTGAATCCTCCGGCACCTCCGGTAAAAGCCTCATGGGTGCACAAAACCGGCTCCACCGGCGGATTCGGCAGCTATGTGGCCTTTATCCCGGAGAAGCAGCTTGGCATCGTGATGCTGGCGAACAAGAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007900", "ARO_id": "46692", "ARO_name": "ACT-118", "CARD_short_name": "ACT-118", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-118.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7319": {"model_id": "7319", "model_name": "ACT-119", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10146": {"protein_sequence": {"accession": "WEY36198.1", "sequence": "MMKKSLCCALLLGISCSALAAPVSDKQLAQVVADTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADVAANKPVTPDTLFELGSISKTFTGVLGGDAVARGEISLGDPVTKYWPELTGTQWQGIRMLDLATYTTGGLPLQVPDEVTDDASLLRFCQRWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPEAEEKNYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMAGWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVVEGSDGKVALAALPAVEVIPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVDAGYRILSALK"}, "dna_sequence": {"accession": "OQ642080.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATTTCTTGCTCTGCTCTGGCCGCGCCGGTGTCGGATAAACAGCTGGCGCAGGTGGTCGCGGATACGATTACGCCGCTGATGAAAGCCCAGTCCATTCCCGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTACTACACCTTCGGCAAAGCCGACGTCGCGGCCAACAAACCGGTCACCCCAGATACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTATTGGGTGGGGATGCTGTCGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACAGGCACGCAGTGGCAGGGCATTCGGATGCTGGATCTGGCGACCTACACCACCGGCGGTTTGCCGCTACAGGTACCGGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTGTCAACGGTGGCAGCCGCAGTGGAAGCCGGGCACAACGCGTCTTTATGCAAACGCCAGCATCGGCCTGTTCGGGGCGCTGGCGGTTAAACCTTCCGGCATGCGTTACGAGCAGGCAATGACCGAGCGGGTATTTAAACCGCTGGCGCTGCATCACACCTGGATTAACGTTCCAGAAGCGGAAGAGAAAAATTACGCCTGGGGCTACCGTGACGGTAAAGCCGTTCACGTTTCGCCGGGAATGCTGGACGCGGAAGCCTATGGCGTCAAAACCAACGTGCAGGATATGGCTGGCTGGGTGATGGCAAACATGGCACCGGAGAAGGTCGCTGACGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGGATAGGTTCAATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTGGAGGCCAAAACGGTGGTCGAGGGGAGTGACGGCAAGGTGGCGCTGGCCGCCTTGCCGGCGGTCGAGGTAATTCCTCCGGCACCGCCTGTAAAAGCCTCCTGGGTGCACAAAACCGGATCGACTGGCGGGTTCGGCAGCTACGTGGCCTTTATTCCGGAAAAACAGATCGGCATCGTGATGCTGGCGAATAAAAGTTACCCCAACCCGGCGCGCGTTGACGCGGGTTATCGTATTTTGAGCGCGCTGAAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007901", "ARO_id": "46693", "ARO_name": "ACT-119", "CARD_short_name": "ACT-119", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-119.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7320": {"model_id": "7320", "model_name": "ACT-120", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10147": {"protein_sequence": {"accession": "WLO97150.1", "sequence": "MMKKSLCCALLLSTSCSVFAAPMSDKQLADVVERTITPLMKAQAIPGMAVAVIYQDQPHYFTFGIADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLTDPATKYWPELSGKQWQGIRLLDLATYTAGGLPLQVPDEVTDNASMLRFYQNWQPQWKRGTTRLYANSSIGLFGALAVKPSDMSYAQAMTQRVFKPLALHHTWINVPKAEEEHYAWGYRDGKPVHVSPGALDAEAYGVKSNVQDMASWVMTNMAPENIADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVDAKTVVDGSGNKVALAPLPAVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVEAAYHILDALQ"}, "dna_sequence": {"accession": "OR398187.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCTTGCTCTGTGTTCGCCGCGCCAATGTCAGATAAACAGCTGGCTGACGTGGTGGAACGTACCATTACGCCGTTGATGAAAGCCCAGGCCATTCCAGGAATGGCGGTTGCAGTGATTTATCAGGATCAGCCGCACTACTTTACCTTCGGCATTGCTGATGTCGCGGCGAACAAACCTGTCACCCCGCAAACCTTATTTGAGCTGGGCTCTATTAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAGATTTCACTCACCGATCCGGCCACAAAATACTGGCCAGAATTGTCGGGCAAACAGTGGCAGGGGATTCGCCTGCTCGATCTGGCGACCTATACCGCTGGCGGTCTGCCCTTGCAGGTACCGGACGAGGTTACGGATAACGCCTCTATGCTGCGCTTCTATCAAAACTGGCAGCCACAGTGGAAGCGAGGCACCACGCGCCTTTATGCGAATTCCAGCATTGGTCTTTTTGGTGCACTGGCGGTTAAACCTTCCGACATGAGCTATGCGCAGGCCATGACGCAGCGAGTGTTTAAACCGCTGGCGCTGCATCACACCTGGATTAACGTTCCGAAAGCTGAAGAGGAGCATTACGCCTGGGGCTACCGCGATGGCAAACCGGTACACGTTTCGCCAGGCGCGCTGGACGCTGAAGCCTATGGCGTGAAAAGCAACGTGCAAGATATGGCGAGCTGGGTGATGACAAATATGGCGCCGGAGAACATTGCTGATGCGTCACTTAAGCAAGGGATCGCGCTGGCACAGTCTCGTTACTGGCGCATCGGATCCATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCAGTAGACGCCAAAACTGTAGTCGACGGTAGCGGCAATAAAGTGGCATTAGCACCGCTGCCAGCGGTAGAAGTGAACCCTCCGGCGCCGCCTGTAAAAGCATCATGGGTACATAAAACCGGGTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGTACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007902", "ARO_id": "46694", "ARO_name": "ACT-120", "CARD_short_name": "ACT-120", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-120.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7321": {"model_id": "7321", "model_name": "ACT-121", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10148": {"protein_sequence": {"accession": "WLO97151.1", "sequence": "MMKKSLCCALLLSTSCSVFAAPMSDKQLADVVERTITPLMKAQAIPGMAVAVIYQDQPHYFTFGIADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLTDPATKYWPELSGKQWQGIRLLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSDMSYAQAMTQRVFKPLALHHTWINVPKAEEEHYAWGYRDGKPVHVSPGALDAEAYGVKSNVQDMASWVMTNMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVDAKTVVDGSGNKVALAPLPAVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVEAAYHILDALQ"}, "dna_sequence": {"accession": "OR398188.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCTTGCTCTGTGTTCGCCGCGCCAATGTCAGATAAACAGCTGGCTGACGTGGTGGAACGTACCATTACGCCGTTGATGAAAGCCCAGGCCATTCCAGGAATGGCGGTTGCAGTGATTTATCAGGATCAGCCGCACTACTTTACCTTCGGCATTGCTGATGTCGCGGCGAACAAACCTGTCACCCCGCAAACCTTATTTGAGCTAGGCTCTATTAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAGATTTCACTCACCGATCCGGCCACAAAATACTGGCCAGAATTGTCGGGCAAACAGTGGCAGGGGATTCGCCTGCTCGATCTGGCGACCTATACCGCTGGCGGTCTGCCCTTGCAGGTACCGGACGAGGTTACGGATAATGCCTCTCTGCTGCGCTTCTATCAAAACTGGCAGCCACAGTGGAAGCCAGGCACCACGCGCCTTTATGCGAATTCCAGCATTGGTCTTTTTGGTGCACTGGCGGTTAAACCTTCCGACATGAGCTATGCGCAGGCCATGACGCAGCGAGTGTTTAAACCGCTGGCGCTACATCACACCTGGATTAACGTTCCGAAAGCTGAAGAGGAGCATTACGCCTGGGGCTACCGCGATGGCAAACCGGTACACGTTTCGCCAGGCGCGCTGGACGCTGAAGCCTATGGCGTGAAAAGCAACGTGCAAGATATGGCGAGCTGGGTGATGACAAATATGGCGCCGGAGAACGTTGCTGATGCGTCACTTAAGCAAGGGATCGCGCTGGCACAGTCTCGTTACTGGCGCATCGGATCCATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCAGTAGACGCCAAAACTGTAGTCGACGGTAGCGGCAATAAAGTGGCACTGGCACCGCTGCCAGCGGTAGAAGTGAACCCTCCGGCGCCGCCTGTAAAAGCATCATGGGTACATAAAACCGGGTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGTACGCGTCGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007903", "ARO_id": "46695", "ARO_name": "ACT-121", "CARD_short_name": "ACT-121", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-121.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7322": {"model_id": "7322", "model_name": "ACT-122", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10149": {"protein_sequence": {"accession": "WLO97152.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEMVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "OR398189.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGATGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGTCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACACGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007904", "ARO_id": "46696", "ARO_name": "ACT-122", "CARD_short_name": "ACT-122", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-122.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7323": {"model_id": "7323", "model_name": "ACT-123", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10150": {"protein_sequence": {"accession": "WLO97153.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTHLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "OR398190.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTAGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCATCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007905", "ARO_id": "46697", "ARO_name": "ACT-123", "CARD_short_name": "ACT-123", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-123.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7324": {"model_id": "7324", "model_name": "ACT-124", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10151": {"protein_sequence": {"accession": "WLO97154.1", "sequence": "MMKKSLCCAVLLGISCSALAAPVSQKQLAEVVTNTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARSEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPNEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMVNMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVVEGSDSKVALAALPAVEINPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "OR398191.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCGTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCCGTATCACAAAAACAGCTGGCGGAGGTGGTCACGAATACGATTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTATACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCAGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGAATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGTAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTACCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCAAAAACGGTGGTCGAGGGCAGCGACAGTAAGGTGGCGCTGGCCGCCTTGCCTGCGGTCGAAATAAATCCTCCGGCTCCGCCTGTAAAAGCCTCCTGGGTGCACAAAACCGGGTCGACGGGCGGGTTCGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGCATCGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007906", "ARO_id": "46698", "ARO_name": "ACT-124", "CARD_short_name": "ACT-124", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-124.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7325": {"model_id": "7325", "model_name": "ACT-131", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10152": {"protein_sequence": {"accession": "KUQ42458.1", "sequence": "MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKSEEPHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "LRCI01000124.1", "fmin": "14945", "fmax": "16091", "strand": "-", "sequence": "ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGTCAGAAGAACCGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCCGGCATGCTCGATGCCGAAGCATATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGGGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCACTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTGCATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAGAAGGAACTCGGCATCGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "45936", "NCBI_taxonomy_name": "Enterobacter ludwigii", "NCBI_taxonomy_id": "299767"}}}}, "ARO_accession": "3007907", "ARO_id": "46699", "ARO_name": "ACT-131", "CARD_short_name": "ACT-131", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-131.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7326": {"model_id": "7326", "model_name": "ACT-140", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10153": {"protein_sequence": {"accession": "HDR2669832.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLADMVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVLKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDIASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "DAOHVV010000003.1", "fmin": "383117", "fmax": "384263", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACATGGTAGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATAGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCAAATAAAAGCTACCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007908", "ARO_id": "46700", "ARO_name": "ACT-140", "CARD_short_name": "ACT-140", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-140.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7327": {"model_id": "7327", "model_name": "ACT-141", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10154": {"protein_sequence": {"accession": "KTJ22338.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDALARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "LPPY01000058.1", "fmin": "457269", "fmax": "458415", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCCTTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007909", "ARO_id": "46701", "ARO_name": "ACT-141", "CARD_short_name": "ACT-141", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-141.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7328": {"model_id": "7328", "model_name": "ACT-142", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10155": {"protein_sequence": {"accession": "EMC7919385.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "ABPSFX010000064.1", "fmin": "13703", "fmax": "14849", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACTGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGGCAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTACTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007910", "ARO_id": "46702", "ARO_name": "ACT-142", "CARD_short_name": "ACT-142", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-142.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7329": {"model_id": "7329", "model_name": "ACT-143", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10156": {"protein_sequence": {"accession": "AMZ75637.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVTANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNTSLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMNFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLLVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "CP015227.1", "fmin": "191990", "fmax": "193136", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTACGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACACCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAACTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACTGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47911", "NCBI_taxonomy_name": "Enterobacter sp.", "NCBI_taxonomy_id": "42895"}}}}, "ARO_accession": "3007911", "ARO_id": "46703", "ARO_name": "ACT-143", "CARD_short_name": "ACT-143", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-143.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7330": {"model_id": "7330", "model_name": "ACT-144", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10157": {"protein_sequence": {"accession": "EJK8937280.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"}, "dna_sequence": {"accession": "ABGYLI010000008.1", "fmin": "45899", "fmax": "47045", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCGCAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCATTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007912", "ARO_id": "46704", "ARO_name": "ACT-144", "CARD_short_name": "ACT-144", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-144.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7331": {"model_id": "7331", "model_name": "ACT-145", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10158": {"protein_sequence": {"accession": "AUM01997.1", "sequence": "MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEPHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMANWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "CP020817.3", "fmin": "405091", "fmax": "406237", "strand": "-", "sequence": "ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGCTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGCCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAACTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47911", "NCBI_taxonomy_name": "Enterobacter sp.", "NCBI_taxonomy_id": "42895"}}}}, "ARO_accession": "3007913", "ARO_id": "46705", "ARO_name": "ACT-145", "CARD_short_name": "ACT-145", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-145.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7332": {"model_id": "7332", "model_name": "ACT-146", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10159": {"protein_sequence": {"accession": "EMN8661052.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDSSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "ABMQTZ020000010.1", "fmin": "130659", "fmax": "131805", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACATTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATAAACGTCCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATTCGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTATGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007914", "ARO_id": "46706", "ARO_name": "ACT-146", "CARD_short_name": "ACT-146", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-146.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7333": {"model_id": "7333", "model_name": "ACT-148", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10160": {"protein_sequence": {"accession": "CZY90887.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRTGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "FKAD01000003.1", "fmin": "468418", "fmax": "469564", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCACAGTCGCGCTACTGGCGTACCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007915", "ARO_id": "46707", "ARO_name": "ACT-148", "CARD_short_name": "ACT-148", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-148.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7334": {"model_id": "7334", "model_name": "ACT-150", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10161": {"protein_sequence": {"accession": "UKB65296.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTSVLGGDAIARGEISLDDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "CP091481.1", "fmin": "380303", "fmax": "381449", "strand": "-", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGTACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTAACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCAGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGACGACCCCGTGACAAAGTACTGGCCCGAGTTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007916", "ARO_id": "46708", "ARO_name": "ACT-150", "CARD_short_name": "ACT-150", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-150.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7335": {"model_id": "7335", "model_name": "ACT-151", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10162": {"protein_sequence": {"accession": "MBW7688613.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "JAHZRO010000014.1", "fmin": "19385", "fmax": "20531", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007917", "ARO_id": "46709", "ARO_name": "ACT-151", "CARD_short_name": "ACT-151", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-151.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7336": {"model_id": "7336", "model_name": "ACT-153", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10163": {"protein_sequence": {"accession": "WRT49607.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMNYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "CP141897.1", "fmin": "2650701", "fmax": "2651847", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAACTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007918", "ARO_id": "46710", "ARO_name": "ACT-153", "CARD_short_name": "ACT-153", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-153.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7337": {"model_id": "7337", "model_name": "ACT-154", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10164": {"protein_sequence": {"accession": "UOY66714.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNVQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTLVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKGLGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "CP083828.1", "fmin": "381787", "fmax": "382933", "strand": "-", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACTGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGGCAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGCATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCCTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGGACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007919", "ARO_id": "46711", "ARO_name": "ACT-154", "CARD_short_name": "ACT-154", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-154.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7338": {"model_id": "7338", "model_name": "ACT-155", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10165": {"protein_sequence": {"accession": "UJA58935.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGTLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"}, "dna_sequence": {"accession": "CP090909.1", "fmin": "3158864", "fmax": "3160010", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAACGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007920", "ARO_id": "46712", "ARO_name": "ACT-155", "CARD_short_name": "ACT-155", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-155.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7339": {"model_id": "7339", "model_name": "ACT-156", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10166": {"protein_sequence": {"accession": "MBW8248988.1", "sequence": "MIKKSLCCALLLGVSCSSIAASMTEKQLADVVEKNITPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTQYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDSASLLRFYQTWQPQWKPGTTRLYANASIGLFGALAVKPSGMGFEQAMTKRVFKPLGLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVVANMAPDNVQDASLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVDAAYRILDALQ"}, "dna_sequence": {"accession": "JAHZUV010000006.1", "fmin": "207634", "fmax": "208780", "strand": "+", "sequence": "ATGATCAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCGTGTCATGTTCCAGCATTGCTGCGTCGATGACAGAAAAACAGCTGGCTGACGTGGTGGAAAAAAACATTACCCCCCTGATGAAAGCGCAGTCCATTCCGGGCATGGCGGTTGCCGTGATCTACCAGGGCCAGCCGCACTATTTTACTTTTGGTAAAGCCGATGTTGCCGCGAACAAACCTGTTACCCCACAAACCCTGTTCGAACTGGGTTCTATCAGTAAAACTTTCACCGGCGTATTGGGCGGCGATGCCATTGCCCGCGGTGAAATATCGCTGGGCGATCCGGTGACCCAATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAGGGGATTCGCATGCTGGATCTGGCGACCTATACCGCGGGAGGGTTACCGCTTCAGGTGCCGGACGAGGTGACCGACAGCGCGTCGCTGCTTCGCTTTTACCAGACATGGCAGCCGCAGTGGAAACCGGGCACCACGCGACTGTACGCGAACGCCAGCATCGGTCTGTTTGGCGCACTGGCGGTTAAACCTTCCGGCATGGGCTTTGAACAGGCCATGACGAAGCGGGTCTTTAAACCGCTCGGGCTCGACCATACGTGGATCAACGTTCCGAAAGCAGAAGAGGCACATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTGTCACCGGGGATGCTGGACGCCGAAGCCTACGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGGTGGCCAATATGGCACCGGATAACGTTCAGGATGCATCCCTGAAGCAAGGCATTACGCTGGCACAGTCGCGCTACTGGCGCGTAGGGGCCATGTATCAAGGATTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAACAAGGTCGCGCTGGCCCCCCTGCCTGCGAGAGAAGTGAATCCTCCGGCGCCTCCGGTAAAAGCCTCATGGGTGCACAAAACCGGCTCCACCGGCGGATTCGGCAGCTATGTGGCCTTTATCCCTGAGAAACAGCTTGGCATCGTGATGCTGGCGAACAAGAGCTATCCGAACCCGGCACGCGTTGATGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47908", "NCBI_taxonomy_name": "Enterobacter mori", "NCBI_taxonomy_id": "539813"}}}}, "ARO_accession": "3007921", "ARO_id": "46713", "ARO_name": "ACT-156", "CARD_short_name": "ACT-156", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-156.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7340": {"model_id": "7340", "model_name": "ACT-157", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10167": {"protein_sequence": {"accession": "WYI22699.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKIADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "CP149841.1", "fmin": "420086", "fmax": "421232", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTGAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGATTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007922", "ARO_id": "46714", "ARO_name": "ACT-157", "CARD_short_name": "ACT-157", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-157.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7341": {"model_id": "7341", "model_name": "ACT-158", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10168": {"protein_sequence": {"accession": "MCC4544499.1", "sequence": "MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAITRGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "JAJGSG010000001.1", "fmin": "4450700", "fmax": "4451846", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTACTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007923", "ARO_id": "46715", "ARO_name": "ACT-158", "CARD_short_name": "ACT-158", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-158.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7342": {"model_id": "7342", "model_name": "ACT-159", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10169": {"protein_sequence": {"accession": "MCE1398600.1", "sequence": "MMTKSLCCALLLSTSCSVLAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPRYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALATKPSGMGYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPGALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDAMQ"}, "dna_sequence": {"accession": "JAJSXK010000010.1", "fmin": "18801", "fmax": "19947", "strand": "-", "sequence": "ATGATGACAAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTAGCTGCCCCGATGTCAGAAAAACAGCTGGCTGACGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAAGCCATTCCTGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACGCTACTTTACCTTCGGAAAAGCCGACATCGCGGCGAACAAGCCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGAGGCGATGCCATTGCCCGCGGCGAAATATCGCTGGGCGATCCGGTAACCAAATATTGGCCTGAACTGACAGGCAAGCAGTGGCAGGGAATTCGCATGCTGGATCTGGCAACCTATACAGCAGGAGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCTAATGCCAGCATCGGTTTGTTTGGCGCGCTGGCGACCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTCGACCATACCTGGATTAACGTTCCGAAAGCGGAGGAGGCGCATTACGCCTGGGGATATCGTGACGGTAAAGCAGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCGTATGGCGTGAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGCCAACATGGCCCCTGGCGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCCCGCTACTGGCGCGTGGGTGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGTAAAAACCGTTGTCGGAGGCAGCGATAACAAGGTTGCCCTGGCACCGTTGCCCGCGAGAGAAGTGAATCCTCCGGCGCCTCCGGTAAAAGCCTCATGGGTGCATAAAACCGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATTCTTGACGCGATGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007924", "ARO_id": "46716", "ARO_name": "ACT-159", "CARD_short_name": "ACT-159", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-159.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7343": {"model_id": "7343", "model_name": "ACT-160", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10170": {"protein_sequence": {"accession": "MCK6739931.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLAAVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "JAKMOE010000004.1", "fmin": "493276", "fmax": "494422", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGCCGTGGTAGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATAAACGTCCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTATGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007925", "ARO_id": "46717", "ARO_name": "ACT-160", "CARD_short_name": "ACT-160", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-160.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7344": {"model_id": "7344", "model_name": "ACT-161", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10171": {"protein_sequence": {"accession": "MCO4185007.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVPPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEVAYRILSALQ"}, "dna_sequence": {"accession": "JAIOHD010000008.1", "fmin": "144977", "fmax": "146123", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAAAAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCTGAAGTGCCCCCCCCAGCTCCGCCAGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGTGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007926", "ARO_id": "46718", "ARO_name": "ACT-161", "CARD_short_name": "ACT-161", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-161.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7345": {"model_id": "7345", "model_name": "ACT-162", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10172": {"protein_sequence": {"accession": "MCS4603851.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVPPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "JAHWRE010000025.1", "fmin": "16929", "fmax": "18075", "strand": "-", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAAAAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCTGAAGTGCCCCCCCCAGCTCCGCCAGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007927", "ARO_id": "46719", "ARO_name": "ACT-162", "CARD_short_name": "ACT-162", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-162.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7346": {"model_id": "7346", "model_name": "ACT-165", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10173": {"protein_sequence": {"accession": "MEG5635058.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINIPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPPVKASWVHKTGSTGGFGSYAAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "JAXROJ010000007.1", "fmin": "195157", "fmax": "196303", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTAGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACATCCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGTCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTCCTCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGCGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007928", "ARO_id": "46720", "ARO_name": "ACT-165", "CARD_short_name": "ACT-165", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-165.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7347": {"model_id": "7347", "model_name": "ACT-166", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10174": {"protein_sequence": {"accession": "MEG5532466.1", "sequence": "MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEMSLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKSEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGIQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "JAXRNI010000004.1", "fmin": "14773", "fmax": "15919", "strand": "-", "sequence": "ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACTTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCAAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATGTCGCTGGGCGATCCGGTGACTAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACAGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGTCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGCATACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAAGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCGGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "45936", "NCBI_taxonomy_name": "Enterobacter ludwigii", "NCBI_taxonomy_id": "299767"}}}}, "ARO_accession": "3007929", "ARO_id": "46721", "ARO_name": "ACT-166", "CARD_short_name": "ACT-166", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-166.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7348": {"model_id": "7348", "model_name": "ACT-167", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10175": {"protein_sequence": {"accession": "XAJ73541.1", "sequence": "MMTKSLCYALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVADNASLLRFYQNWQPQWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAITTRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLHDNSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDARTVVEGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740475.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGACAAAATCCCTTTGCTACGCCCTGCTGCTCAGCACCTCCTGCTCAGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAAGTGGTGGAACGGACTGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAGCCTGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGTGTACTGGGTGGCGATGCGATTGCTCGCGGTGAAATATCGCTGGGCGACCCGGTGACCAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGGGGTCTGCCGTTACAGGTACCGGATGAGGTCGCGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATACCAGCATCGGCCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAGGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTCGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTAATGGTCAACATGAAGCCGGACTCCCTTCATGATAATTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAGAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCCGCGAGAGAAGTGAATCCACCAGCGCCTCCGGTAAAAGCCTCATGGGTGCACAAAACCGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47911", "NCBI_taxonomy_name": "Enterobacter sp.", "NCBI_taxonomy_id": "42895"}}}}, "ARO_accession": "3007930", "ARO_id": "46722", "ARO_name": "ACT-167", "CARD_short_name": "ACT-167", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-167.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7349": {"model_id": "7349", "model_name": "ACT-168", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10176": {"protein_sequence": {"accession": "XAJ73542.1", "sequence": "MMKKNLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEITLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPKWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMMPDSLQDSPLKHGIALAQSRYWRVGSMYQGLGWEMLNWPVDAQTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740476.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAAAACCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCTGATGTTGCAGCGAACAAACCCGTCACCCCGCAAACCTTGTTCGAGCTGGGTTCGATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCGCGCGGTGAAATAACGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGCCTGCCGTTGCAGGTGCCGGATGAGGTCACGGATACCGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCAAAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACACCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCCTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTATTTAAGCCGCTCAAGCTGGACCATACATGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAATATGATGCCGGACTCCCTTCAGGATTCCCCACTTAAACACGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGATCCATGTATCAAGGATTGGGCTGGGAAATGCTGAACTGGCCGGTCGACGCCCAAACGGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCAAGAGAAGTGAATCCACCGGCACCACCGGTTAAGGCCTCCTGGGTCCATAAAACGGGCTCTACCGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47909", "NCBI_taxonomy_name": "Enterobacter quasiroggenkampii", "NCBI_taxonomy_id": "2497436"}}}}, "ARO_accession": "3007931", "ARO_id": "46723", "ARO_name": "ACT-168", "CARD_short_name": "ACT-168", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-168.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7350": {"model_id": "7350", "model_name": "ACT-169", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10177": {"protein_sequence": {"accession": "XAJ73543.1", "sequence": "MKTKSLCCALMLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTFVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "PP740477.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCTTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007932", "ARO_id": "46724", "ARO_name": "ACT-169", "CARD_short_name": "ACT-169", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-169.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7351": {"model_id": "7351", "model_name": "ACT-170", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10178": {"protein_sequence": {"accession": "XAJ73544.1", "sequence": "MMKKFLCCALLLNTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAISRGEISMGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTARVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740478.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAACACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTTCCCGCGGCGAAATTTCGATGGGCGATCCGGTAACTAAATATTGGCCTGAACTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGGCGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAACATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTCCCCTGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007933", "ARO_id": "46725", "ARO_name": "ACT-170", "CARD_short_name": "ACT-170", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-170.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7352": {"model_id": "7352", "model_name": "ACT-171", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10179": {"protein_sequence": {"accession": "XAJ73545.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDARAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740479.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACGAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007934", "ARO_id": "46726", "ARO_name": "ACT-171", "CARD_short_name": "ACT-171", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-171.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7353": {"model_id": "7353", "model_name": "ACT-172", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10180": {"protein_sequence": {"accession": "XAJ73546.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVLKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740480.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007935", "ARO_id": "46727", "ARO_name": "ACT-172", "CARD_short_name": "ACT-172", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-172.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7354": {"model_id": "7354", "model_name": "ACT-173", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10181": {"protein_sequence": {"accession": "XAJ73547.1", "sequence": "MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKTEEAHYAWGYSDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVDAAYRILSAL"}, "dna_sequence": {"accession": "PP740481.1", "fmin": "0", "fmax": "1143", "strand": "+", "sequence": "ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGTTGATGAATGCGCAGGCCATCCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAACCCGTTACCCCACAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTCGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACGGGCAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAAGTCACGGATAACGCCGCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCACTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACAGCGACGGTAAAGCGGTCCACGTTTCGCCAGGAATGCTGGATGCGGAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGCAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCTACCGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTAATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGATGCGGCATACCGTATTTTGAGCGCGCTGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47911", "NCBI_taxonomy_name": "Enterobacter sp.", "NCBI_taxonomy_id": "42895"}}}}, "ARO_accession": "3007936", "ARO_id": "46728", "ARO_name": "ACT-173", "CARD_short_name": "ACT-173", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-173.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7355": {"model_id": "7355", "model_name": "ACT-174", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10182": {"protein_sequence": {"accession": "XAJ73548.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQSIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYYILEALQ"}, "dna_sequence": {"accession": "PP740482.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGAGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACTATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007937", "ARO_id": "46729", "ARO_name": "ACT-174", "CARD_short_name": "ACT-174", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-174.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7356": {"model_id": "7356", "model_name": "ACT-175", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10183": {"protein_sequence": {"accession": "XAJ73549.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSSMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740483.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACATTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCAGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGATGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACAGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCTTGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007938", "ARO_id": "46730", "ARO_name": "ACT-175", "CARD_short_name": "ACT-175", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-175.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7357": {"model_id": "7357", "model_name": "ACT-176", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10184": {"protein_sequence": {"accession": "XAJ73550.1", "sequence": "MMKKSLCCALLLSVACSAFAAPMSEKQLAKVVERAVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTARLYANASIGLFGALAVKPSGMSFEEAMTKRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGIKTNVKDMASWVVANMAPDALQDSSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"}, "dna_sequence": {"accession": "PP740484.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTATGTTGTGCCCTGCTGCTCAGCGTTGCCTGCTCTGCCTTCGCCGCCCCCATGTCAGAAAAACAGCTGGCTAAGGTGGTGGAGCGTGCCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCGCACTACTTTACCTTTGGTAAAGCGGATGTCGCGGCGAATAAACCTGTTACGCCTCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCATTGCTCGCGGTGAAATCTCACTGGGCGATCCAGTGACAAGGTACTGGCCTGAGCTGACAGGAAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGGGGGTTGCCGTTACAGGTACCGGATGACGTCACTGACAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCGCGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGTGCTCTCGCGGTTAAACCCTCCGGCATGAGTTTTGAAGAGGCCATGACGAAGCGGGTCTTTAAGCCGCTCAGGCTCGACCATACGTGGATTAACGTACCAAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCTCCAGGGATGCTGGACGCTGAAGCCTATGGCATAAAAACCAACGTGAAAGATATGGCGAGCTGGGTGGTGGCAAACATGGCCCCCGATGCCCTTCAGGATAGCTCTCTCAAACAAGGGATAGCCCTGGCACAGTCCCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTGAACTGGCCGGTCGATGCCAAAACCGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCCAGAGAAGTCAATCCCCCGGCACCGCCGGTTAAGGCCTCCTGGGTACACAAAACGGGTTCAACCGGTGGGTTTGGGAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47910", "NCBI_taxonomy_name": "Enterobacter sichuanensis", "NCBI_taxonomy_id": "2071710"}}}}, "ARO_accession": "3007939", "ARO_id": "46731", "ARO_name": "ACT-176", "CARD_short_name": "ACT-176", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-176.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7358": {"model_id": "7358", "model_name": "ACT-177", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10185": {"protein_sequence": {"accession": "XAJ73551.1", "sequence": "MMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKADEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDARTVVEGSDNKAALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"}, "dna_sequence": {"accession": "PP740485.1", "fmin": "0", "fmax": "1143", "strand": "+", "sequence": "ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGACGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAGAACCGTGGTTGAAGGTAGCGACAATAAGGCGGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTAGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36926", "NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645"}}}}, "ARO_accession": "3007940", "ARO_id": "46732", "ARO_name": "ACT-177", "CARD_short_name": "ACT-177", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-177.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7359": {"model_id": "7359", "model_name": "ACT-178", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10186": {"protein_sequence": {"accession": "XAJ73552.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTAVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGDLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740486.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGCCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGACCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007941", "ARO_id": "46733", "ARO_name": "ACT-178", "CARD_short_name": "ACT-178", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-178.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7360": {"model_id": "7360", "model_name": "ACT-179", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10187": {"protein_sequence": {"accession": "XAJ73553.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPSVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNLARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740487.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCTCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCTGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007942", "ARO_id": "46734", "ARO_name": "ACT-179", "CARD_short_name": "ACT-179", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-179.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7361": {"model_id": "7361", "model_name": "ACT-180", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10188": {"protein_sequence": {"accession": "XAJ73554.1", "sequence": "MMKKSLSCALLLSVACSAFAAPMSEKQLAKVVERAVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTARLYANASIGLFGALAVKPSGMSFEEAMTKRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGIKTNVKDMASWVVANMAPDALQDSSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"}, "dna_sequence": {"accession": "PP740488.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTAAGTTGTGCCCTGCTGCTCAGCGTTGCCTGCTCTGCCTTCGCCGCCCCCATGTCAGAAAAACAGCTGGCTAAGGTGGTGGAGCGTGCCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCGCACTACTTTACCTTTGGTAAAGCGGATGTCGCGGCGAATAAACCTGTTACGCCTCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCTCGCGGTGAAATCTCACTGGGTGATCCAGTGACAAGGTACTGGCCTGAACTGACAGGAAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGGGGGTTGCCGTTACAGGTACCGGATGACGTCACTGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCGCGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGTGCTCTCGCGGTTAAACCCTCCGGCATGAGTTTTGAAGAGGCCATGACGAAGCGGGTCTTTAAGCCGCTCAGGCTCGACCATACGTGGATTAACGTACCAAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCTCCAGGGATGCTGGACGCTGAAGCCTATGGCATAAAAACCAACGTGAAAGATATGGCGAGCTGGGTGGTGGCAAACATGGCCCCCGATGCCCTTCAGGATAGCTCTCTCAAACAAGGGATAGCCCTGGCACAGTCCCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTGAACTGGCCGGTCGATGCCAAAACCGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCCAGAGAAGTCAATCCCCCGGTACCGCCGGTTAAGGCCTCCTGGGTACACAAAACGGGTTCAACCGGTGGGTTTGGGAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47910", "NCBI_taxonomy_name": "Enterobacter sichuanensis", "NCBI_taxonomy_id": "2071710"}}}}, "ARO_accession": "3007943", "ARO_id": "46735", "ARO_name": "ACT-180", "CARD_short_name": "ACT-180", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-180.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7362": {"model_id": "7362", "model_name": "ACT-181", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10189": {"protein_sequence": {"accession": "XAJ73555.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTSVLGGDAIARGEISLDDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYADASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "PP740489.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGTACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTAACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCAGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGACGACCCCGTGACAAAGTACTGGCCCGAGTTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGGACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007944", "ARO_id": "46736", "ARO_name": "ACT-181", "CARD_short_name": "ACT-181", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-181.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7363": {"model_id": "7363", "model_name": "ACT-182", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10190": {"protein_sequence": {"accession": "XAJ73556.1", "sequence": "MMTKSLCCALLLSTSCSVLAAPMSEKQLAEMVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVLLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740490.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGATGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCTGTCACTCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGTATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCCAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAATATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCAAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAATGCGTCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGTTGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36926", "NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645"}}}}, "ARO_accession": "3007945", "ARO_id": "46737", "ARO_name": "ACT-182", "CARD_short_name": "ACT-182", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-182.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7364": {"model_id": "7364", "model_name": "ACT-183", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10191": {"protein_sequence": {"accession": "XAJ73557.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAVNKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740491.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGTGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007946", "ARO_id": "46738", "ARO_name": "ACT-183", "CARD_short_name": "ACT-183", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-183.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7365": {"model_id": "7365", "model_name": "ACT-184", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10192": {"protein_sequence": {"accession": "XAJ73558.1", "sequence": "MMKKSLCCALLLGLSCSVLAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740492.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGTTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCTGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007947", "ARO_id": "46739", "ARO_name": "ACT-184", "CARD_short_name": "ACT-184", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-184.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7366": {"model_id": "7366", "model_name": "ACT-185", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10193": {"protein_sequence": {"accession": "XAJ73559.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQDWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEDEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEVAYRILSALQ"}, "dna_sequence": {"accession": "PP740493.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTAGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAAGACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGACGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGTGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007948", "ARO_id": "46740", "ARO_name": "ACT-185", "CARD_short_name": "ACT-185", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-185.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7367": {"model_id": "7367", "model_name": "ACT-186", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10194": {"protein_sequence": {"accession": "XAJ73560.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWHIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740494.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCATATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCACCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007949", "ARO_id": "46741", "ARO_name": "ACT-186", "CARD_short_name": "ACT-186", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-186.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7368": {"model_id": "7368", "model_name": "ACT-187", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10195": {"protein_sequence": {"accession": "XAJ73561.1", "sequence": "MMKKTLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTNTASLLRFYQNWQPKWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMMPDSLQDSPLKHGIALAQSRYWRVGAMYQGLGWEMLNWPVDAQTVVGGSDNKEALAPLPAREVNPPAPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740495.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAGAAAACCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGCACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCTGATGTTGCAGCGAACAAACCTGTCACCCCGCAAACCTTGTTCGAGCTGGGTTCGATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCGCGCGGTGAAATAGCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTGCAGGTGCCGGATGAGGTCACGAATACCGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCAAAGTGGAAGCCGGGCACCACGCGGCTTTACGCTAACACCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCCTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGATGCCGGACTCCCTTCAGGATTCCCCACTTAAGCACGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGAGCCATGTATCAAGGATTGGGCTGGGAAATGCTGAACTGGCCGGTCGACGCCCAAACGGTGGTCGGGGGCAGCGACAATAAGGAGGCGCTGGCGCCGTTGCCTGCAAGAGAAGTGAATCCACCGGCACCACTGGTTAAGGCCTCCTGGGTCCATAAAACGGGCTCTACCGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47909", "NCBI_taxonomy_name": "Enterobacter quasiroggenkampii", "NCBI_taxonomy_id": "2497436"}}}}, "ARO_accession": "3007950", "ARO_id": "46742", "ARO_name": "ACT-187", "CARD_short_name": "ACT-187", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-187.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7369": {"model_id": "7369", "model_name": "ACT-188", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10196": {"protein_sequence": {"accession": "XAJ73562.1", "sequence": "MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVAPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "PP740496.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAACTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACTAAATATTGGCCTGAACTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTATACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAACATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTTGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTGCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTATGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47906", "NCBI_taxonomy_name": "Enterobacter bugandensis", "NCBI_taxonomy_id": "881260"}}}}, "ARO_accession": "3007951", "ARO_id": "46743", "ARO_name": "ACT-188", "CARD_short_name": "ACT-188", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-188.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7370": {"model_id": "7370", "model_name": "ACT-189", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10197": {"protein_sequence": {"accession": "XAJ73563.1", "sequence": "MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWIHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740497.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCCTGCTCTGCTCTCGCCGCGCCAGTATCGGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCGCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCACAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAAATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTGGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGATCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGTTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007952", "ARO_id": "46744", "ARO_name": "ACT-189", "CARD_short_name": "ACT-189", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-189.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7371": {"model_id": "7371", "model_name": "ACT-190", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10198": {"protein_sequence": {"accession": "XAJ73564.1", "sequence": "MKTKSLFCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWLELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "PP740498.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTTCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCTGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCTCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCTCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGTTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39773", "NCBI_taxonomy_name": "Enterobacter kobei", "NCBI_taxonomy_id": "208224"}}}}, "ARO_accession": "3007953", "ARO_id": "46745", "ARO_name": "ACT-190", "CARD_short_name": "ACT-190", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-190.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7372": {"model_id": "7372", "model_name": "ACT-191", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10199": {"protein_sequence": {"accession": "XAJ73565.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFEPGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRTGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740499.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCCGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCACAGTCGCGCTACTGGCGTACCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007954", "ARO_id": "46746", "ARO_name": "ACT-191", "CARD_short_name": "ACT-191", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-191.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7373": {"model_id": "7373", "model_name": "ACT-192", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10200": {"protein_sequence": {"accession": "XAJ73566.1", "sequence": "MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDDKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIDGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"}, "dna_sequence": {"accession": "PP740500.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTATACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGATAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGACGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007955", "ARO_id": "46747", "ARO_name": "ACT-192", "CARD_short_name": "ACT-192", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-192.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7374": {"model_id": "7374", "model_name": "ACT-193", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10201": {"protein_sequence": {"accession": "XAJ73567.1", "sequence": "MMKKSLSCALLLSVACSAFAAPMSEKQLAKVVERAVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEEAMTKRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGIKTNVKDMASWVVANMAPDALQDSSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"}, "dna_sequence": {"accession": "PP740501.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTAAGTTGTGCCCTGCTGCTCAGCGTTGCCTGCTCTGCCTTCGCCGCCCCCATGTCAGAAAAACAGCTGGCTAAGGTGGTGGAGCGTGCCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCGCACTACTTTACCTTTGGTAAAGCGGATGTCGCGGCGAATAAACCTGTTACGCCTCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCTCGCGGTGAAATCTCACTGGGCGATCCAGTGACAAGGTACTGGCCTGAGCTGACAGGAAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGTGGGTTGCCGTTACAGGTACCGGATGACGTCACTGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAATGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGTATCGGTCTTTTTGGTGCTCTCGCGGTTAAACCCTCCGGCATGAGTTTTGAAGAGGCCATGACGAAGCGGGTCTTTAAGCCGCTCAGGCTCGACCATACGTGGATTAACGTACCAAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCTCCAGGGATGCTGGACGCTGAAGCCTATGGCATAAAAACCAACGTGAAAGATATGGCGAGCTGGGTGGTGGCAAACATGGCCCCCGATGCCCTTCAGGATAGCTCTCTCAAACAAGGGATAGCCCTGGCACAGTCCCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTGAACTGGCCGGTCGATGCCAAAACCGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCAAGAGAAGTCAATCCCCCGGCACCGCCGGTTAAGGCCTCCTGGGTTCACAAAACGGGTTCTACCGGTGGGTTTGGGAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGTTATCCGAATCCGGCACGCGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "47910", "NCBI_taxonomy_name": "Enterobacter sichuanensis", "NCBI_taxonomy_id": "2071710"}}}}, "ARO_accession": "3007956", "ARO_id": "46748", "ARO_name": "ACT-193", "CARD_short_name": "ACT-193", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-193.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7375": {"model_id": "7375", "model_name": "ACT-194", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10202": {"protein_sequence": {"accession": "XAJ73568.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVKANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "PP740502.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCAAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGAAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007957", "ARO_id": "46749", "ARO_name": "ACT-194", "CARD_short_name": "ACT-194", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-194.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7376": {"model_id": "7376", "model_name": "ACT-85", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10203": {"protein_sequence": {"accession": "MRN75760.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMVNMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "WJXX01000007.1", "fmin": "19311", "fmax": "20451", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACACGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGTAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007958", "ARO_id": "46750", "ARO_name": "ACT-85", "CARD_short_name": "ACT-85", "ARO_description": "Ceftazidime-hydrolyzing class C beta-lactamase ACT-85.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7377": {"model_id": "7377", "model_name": "ACT-86", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10204": {"protein_sequence": {"accession": "MPV43777.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "WHOQ01000125.1", "fmin": "30718", "fmax": "31858", "strand": "-", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGATGGTAAAGCGGTGCGTGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007959", "ARO_id": "46751", "ARO_name": "ACT-86", "CARD_short_name": "ACT-86", "ARO_description": "Ceftazidime-hydrolyzing class C beta-lactamase ACT-86.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7378": {"model_id": "7378", "model_name": "ACT-88", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10205": {"protein_sequence": {"accession": "QTV32571.1", "sequence": "MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLHFYQSWQPQWAPGTMRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMANMAPDGVQDTSLKQGMVFAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "MW887657.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCCGCGAATACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGTAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGATCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCATTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCATGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCAGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGATGGCTAACATGGCCCCCGATGGGGTACAGGATACCTCACTGAAGCAGGGCATGGTGTTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "45936", "NCBI_taxonomy_name": "Enterobacter ludwigii", "NCBI_taxonomy_id": "299767"}}}}, "ARO_accession": "3007960", "ARO_id": "46752", "ARO_name": "ACT-88", "CARD_short_name": "ACT-88", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-88.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7379": {"model_id": "7379", "model_name": "ACT-89", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10206": {"protein_sequence": {"accession": "QUR41147.1", "sequence": "MMRKSLCCALLLGISCSALATPVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "MZ067484.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAGAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACATTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATGCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007961", "ARO_id": "46753", "ARO_name": "ACT-89", "CARD_short_name": "ACT-89", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-89.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7380": {"model_id": "7380", "model_name": "ACT-90", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10207": {"protein_sequence": {"accession": "ESM21743.1", "sequence": "MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADTAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVEASWVHKMGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"}, "dna_sequence": {"accession": "AYIM01000001.1", "fmin": "557504", "fmax": "558650", "strand": "-", "sequence": "ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATACCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTTCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCGAAGCGTCCTGGGTCCATAAAATGGGCTCTACTGGCGGGTTTGGCAGTTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39098", "NCBI_taxonomy_name": "Enterobacter hormaechei", "NCBI_taxonomy_id": "158836"}}}}, "ARO_accession": "3007962", "ARO_id": "46754", "ARO_name": "ACT-90", "CARD_short_name": "ACT-90", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-90.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7381": {"model_id": "7381", "model_name": "ACT-91", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10208": {"protein_sequence": {"accession": "UEG31054.1", "sequence": "MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKAVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKTEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLPDTSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVKGSDNKVALAPLTAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "OL351615.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATCCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAAGCTGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTCCACGTTTCGCCAGGAATGCTGGATGCAGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTTAATATGAAGCCAGACTCCCTCCCGGATACTTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAAGGGTTAGGTTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTAAAGGTAGCGACAATAAGGTAGCGCTGGCACCGCTGACCGCGAGAGAAGTGAATCCGCCGGCACCGCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCTGCCCGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007963", "ARO_id": "46755", "ARO_name": "ACT-91", "CARD_short_name": "ACT-91", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-91.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7382": {"model_id": "7382", "model_name": "ACT-92", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10209": {"protein_sequence": {"accession": "UEG31055.1", "sequence": "MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMANWVIVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTDSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "OL351616.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCAGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAATAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAACTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAACTGGGTGATAGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGACTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007964", "ARO_id": "46756", "ARO_name": "ACT-92", "CARD_short_name": "ACT-92", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-92.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7383": {"model_id": "7383", "model_name": "ACT-93", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10210": {"protein_sequence": {"accession": "UEG31057.1", "sequence": "MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQVIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQTITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}, "dna_sequence": {"accession": "OL351618.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCTCAGGTCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCCGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGACCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCGTTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007965", "ARO_id": "46757", "ARO_name": "ACT-93", "CARD_short_name": "ACT-93", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-93.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7384": {"model_id": "7384", "model_name": "ACT-94", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10211": {"protein_sequence": {"accession": "UEG31058.1", "sequence": "MMKKSLCCALLLGVSCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKSGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "OL351619.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCGTCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGAGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGTCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007966", "ARO_id": "46758", "ARO_name": "ACT-94", "CARD_short_name": "ACT-94", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-94.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7385": {"model_id": "7385", "model_name": "ACT-95", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10212": {"protein_sequence": {"accession": "UHK14138.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794635.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGTTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007967", "ARO_id": "46759", "ARO_name": "ACT-95", "CARD_short_name": "ACT-95", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-95.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7386": {"model_id": "7386", "model_name": "ACT-96", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10213": {"protein_sequence": {"accession": "UHK14141.1", "sequence": "MKTKSLCCALMLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMNFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAFRILSALQ"}, "dna_sequence": {"accession": "OL794638.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAACTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATTCCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007968", "ARO_id": "46760", "ARO_name": "ACT-96", "CARD_short_name": "ACT-96", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-96.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7387": {"model_id": "7387", "model_name": "ACT-97", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10214": {"protein_sequence": {"accession": "UHK14144.1", "sequence": "MKTKSLCCALMLSTSCSVLAAPMSEKQLSNVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794641.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTAACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007969", "ARO_id": "46761", "ARO_name": "ACT-97", "CARD_short_name": "ACT-97", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-97.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7388": {"model_id": "7388", "model_name": "ACT-98", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10215": {"protein_sequence": {"accession": "UHK14151.1", "sequence": "MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEDEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKKLGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794648.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCTCTTTGCTGTGCCCTGCTGCTCAGCACCTCTTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGACGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGAAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007970", "ARO_id": "46762", "ARO_name": "ACT-98", "CARD_short_name": "ACT-98", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-98.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7389": {"model_id": "7389", "model_name": "ACT-99", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10216": {"protein_sequence": {"accession": "UHK14152.1", "sequence": "MKTKSLCSALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVESKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"}, "dna_sequence": {"accession": "OL794649.1", "fmin": "0", "fmax": "1146", "strand": "+", "sequence": "ATGAAGACAAAATCCCTTTGCAGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACTGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGGCAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAATCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007971", "ARO_id": "46763", "ARO_name": "ACT-99", "CARD_short_name": "ACT-99", "ARO_description": "Cephalosporin-hydrolyzing class C beta-lactamase ACT-99.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7390": {"model_id": "7390", "model_name": "ACT-GC1", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10217": {"protein_sequence": {"accession": "BAA07922.1", "sequence": "MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"}, "dna_sequence": {"accession": "D44479.1", "fmin": "389", "fmax": "1544", "strand": "+", "sequence": "ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36884", "NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550"}}}}, "ARO_accession": "3007972", "ARO_id": "46764", "ARO_name": "ACT-GC1", "CARD_short_name": "ACT-GC1", "ARO_description": "Extended spectrum class C beta-lactamase ACT-GC1.", "ARO_category": {"36211": {"category_aro_accession": "3000072", "category_aro_cvterm_id": "36211", "category_aro_name": "ACT beta-lactamase", "category_aro_description": "ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7391": {"model_id": "7391", "model_name": "ADC-257", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10218": {"protein_sequence": {"accession": "QVU28095.1", "sequence": "MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"}, "dna_sequence": {"accession": "MZ224611.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007973", "ARO_id": "46765", "ARO_name": "ADC-257", "CARD_short_name": "ADC-257", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-257.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7392": {"model_id": "7392", "model_name": "ADC-258", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10219": {"protein_sequence": {"accession": "QVU28094.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "MZ224612.1", "fmin": "0", "fmax": "1167", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007974", "ARO_id": "46766", "ARO_name": "ADC-258", "CARD_short_name": "ADC-258", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-258.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7393": {"model_id": "7393", "model_name": "ADC-259", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10220": {"protein_sequence": {"accession": "UBX38689.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPSPLDAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OK340849.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCAGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007975", "ARO_id": "46767", "ARO_name": "ADC-259", "CARD_short_name": "ADC-259", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-259.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7394": {"model_id": "7394", "model_name": "ADC-260", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10221": {"protein_sequence": {"accession": "UCZ39549.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGSLGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OK396701.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCTCACTCGGTGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007976", "ARO_id": "46768", "ARO_name": "ADC-260", "CARD_short_name": "ADC-260", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-260.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7395": {"model_id": "7395", "model_name": "ADC-261", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10222": {"protein_sequence": {"accession": "UGW32408.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPIEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OL774887.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAATTGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007977", "ARO_id": "46769", "ARO_name": "ADC-261", "CARD_short_name": "ADC-261", "ARO_description": "Cefepime-hydrolyzing class C beta-lactamase ADC-261.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7396": {"model_id": "7396", "model_name": "ADC-262", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10223": {"protein_sequence": {"accession": "UHO07582.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"}, "dna_sequence": {"accession": "OL901271.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007978", "ARO_id": "46770", "ARO_name": "ADC-262", "CARD_short_name": "ADC-262", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-262.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7397": {"model_id": "7397", "model_name": "ADC-263", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10224": {"protein_sequence": {"accession": "UHO07583.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTLFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OL901272.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTGTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007979", "ARO_id": "46771", "ARO_name": "ADC-263", "CARD_short_name": "ADC-263", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-263.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7398": {"model_id": "7398", "model_name": "ADC-264", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10225": {"protein_sequence": {"accession": "UHO07591.1", "sequence": "MRFIKISCLLLPSLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLRSVQDKKVVNGSTIFELGSVSKLFTAKAGGYAKTKGKISFEDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKEWKPKNQIGEYRQYSNPSIGLFGKIVGLSMNQPFSQVLEKTIFPSLHLKNSYVNVPKIQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLSFIDANLNPQKYPADIRRAIDETHKGFYQIGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKSNKVTAISKEPSIKIFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OL901280.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTATAAAAATTTCCTGCTTACTTTTACCGTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACACCAAAAGAGCAAGAAATTAAAAAACTGGTTGATCAAAACTTTAAACCTTTATTAGAAAAATATGATGTGCCCGGTATGGCGGTGGGCGTTATTCAAAATAATAAAAAGTATGAAATCTATTATGGTTTAAGATCCGTTCAAGATAAAAAAGTTGTAAATGGTAGTACTATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCGAAGGCAGGCGGCTATGCAAAAACAAAAGGAAAAATCTCTTTTGAAGACACCCCAGGAAAATACTGGAAAGAACTAAAAAACACGCCTATTGATCAGGTCAATCTACTTCAACTTGCTACATATACGAGTGGCAACCTTGGCTTACAATTCCCAGATGAAGTACAAACAGACCAGCAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAATCAAATCGGTGAATATCGGCAATATTCAAACCCAAGTATTGGCTTATTTGGAAAAATTGTAGGCTTATCGATGAATCAGCCTTTTAGTCAGGTTTTAGAAAAGACAATTTTTCCGTCTCTTCACTTAAAAAATAGCTATGTAAATGTGCCTAAAATTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTACCCCAGGCCCACTCGATGCCCCTGCCTACGGGGTTAAATCTACATTACCAGACATGCTTAGCTTTATTGATGCCAATCTAAATCCACAAAAATATCCAGCAGATATTCGACGCGCAATTGATGAGACTCATAAAGGTTTTTATCAAATCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCCCCTTTACAAACTTTATTAGACAGTAACTCTGAACAAATTGTGATGAAATCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATCAAAATATTCCATAAAACGGGTTCAACTAATGGATTTGGAACTTATGTTGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGTATTAAAGCGGCTTACGCTGTATTGAATGCGATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39094", "NCBI_taxonomy_name": "Acinetobacter calcoaceticus", "NCBI_taxonomy_id": "471"}}}}, "ARO_accession": "3007980", "ARO_id": "46772", "ARO_name": "ADC-264", "CARD_short_name": "ADC-264", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-264.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7399": {"model_id": "7399", "model_name": "ADC-265", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10226": {"protein_sequence": {"accession": "ULU82599.1", "sequence": "MRFKKISCLLLPPLFIFSTSIYAGNTPKEQEVKKLIDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQHAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OM572561.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGCCTACTTTTACCGCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGAAACACCCCCAAAGAACAAGAAGTTAAAAAACTGATAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCTGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTAATGACACACCCGGAAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAACCTTGCTTTGCAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAACGTACCTAAAACTCAAATGCAAAATTATGCATATGGCTATAATCAAGAAAATCAGCCGATCCGAGTTAACCCTGGCCCGCTAGATGCCCCTGCGTACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACATGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36787", "NCBI_taxonomy_name": "Acinetobacter pittii", "NCBI_taxonomy_id": "48296"}}}}, "ARO_accession": "3007981", "ARO_id": "46773", "ARO_name": "ADC-265", "CARD_short_name": "ADC-265", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-265.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7400": {"model_id": "7400", "model_name": "ADC-266", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10227": {"protein_sequence": {"accession": "UOU25744.1", "sequence": "MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGIIQNNKKYEAYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKDNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON191578.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTACCGGGTATGGCGGTAGGTATTATTCAAAACAATAAAAAATATGAAGCGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACACCGGGCAAATACTGGAAAGAGTTAAAAAACACTCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCTTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAATCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACCAATGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGACAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36949", "NCBI_taxonomy_name": "Acinetobacter nosocomialis", "NCBI_taxonomy_id": "106654"}}}}, "ARO_accession": "3007982", "ARO_id": "46774", "ARO_name": "ADC-266", "CARD_short_name": "ADC-266", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-266.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7401": {"model_id": "7401", "model_name": "ADC-267", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10228": {"protein_sequence": {"accession": "UTQ48801.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"}, "dna_sequence": {"accession": "ON960904.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007983", "ARO_id": "46775", "ARO_name": "ADC-267", "CARD_short_name": "ADC-267", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-267.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7402": {"model_id": "7402", "model_name": "ADC-268", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10229": {"protein_sequence": {"accession": "UTS94213.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651460.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007984", "ARO_id": "46776", "ARO_name": "ADC-268", "CARD_short_name": "ADC-268", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-268.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7403": {"model_id": "7403", "model_name": "ADC-269", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10230": {"protein_sequence": {"accession": "UTS94214.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQALEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"}, "dna_sequence": {"accession": "ON651461.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGCCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007985", "ARO_id": "46777", "ARO_name": "ADC-269", "CARD_short_name": "ADC-269", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-269.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7404": {"model_id": "7404", "model_name": "ADC-270", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10231": {"protein_sequence": {"accession": "UTS94215.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTMFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPKDIQRAINETHQGFYQVNTMYQALGWEDFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651462.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCTGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATGTTTCCGGCTCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGATTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007986", "ARO_id": "46778", "ARO_name": "ADC-270", "CARD_short_name": "ADC-270", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-270.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7405": {"model_id": "7405", "model_name": "ADC-271", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10232": {"protein_sequence": {"accession": "UTS94216.1", "sequence": "MRFKKISCLLFSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTMFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651463.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTCTCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATGTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTGGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGATTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007987", "ARO_id": "46779", "ARO_name": "ADC-271", "CARD_short_name": "ADC-271", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-271.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7406": {"model_id": "7406", "model_name": "ADC-272", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10233": {"protein_sequence": {"accession": "UTS94217.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNNSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651464.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAACAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007988", "ARO_id": "46780", "ARO_name": "ADC-272", "CARD_short_name": "ADC-272", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-272.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7407": {"model_id": "7407", "model_name": "ADC-273", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10234": {"protein_sequence": {"accession": "UTS94218.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFNPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651465.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAATCCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCTCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007989", "ARO_id": "46781", "ARO_name": "ADC-273", "CARD_short_name": "ADC-273", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-273.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7408": {"model_id": "7408", "model_name": "ADC-274", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10235": {"protein_sequence": {"accession": "UTS94219.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651466.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007990", "ARO_id": "46782", "ARO_name": "ADC-274", "CARD_short_name": "ADC-274", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-274.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7409": {"model_id": "7409", "model_name": "ADC-275", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10236": {"protein_sequence": {"accession": "UTS94220.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPNDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651467.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAATGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007991", "ARO_id": "46783", "ARO_name": "ADC-275", "CARD_short_name": "ADC-275", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-275.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7410": {"model_id": "7410", "model_name": "ADC-276", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10237": {"protein_sequence": {"accession": "UTS94221.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYIQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"}, "dna_sequence": {"accession": "ON651468.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACATACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007992", "ARO_id": "46784", "ARO_name": "ADC-276", "CARD_short_name": "ADC-276", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-276.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7411": {"model_id": "7411", "model_name": "ADC-277", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10238": {"protein_sequence": {"accession": "UTS94222.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKFVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSGDCSKFCVST"}, "dna_sequence": {"accession": "ON651469.1", "fmin": "0", "fmax": "1170", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGTTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGGGGACTGTTCTAAATTTTGTGTAAGTACTTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007993", "ARO_id": "46785", "ARO_name": "ADC-277", "CARD_short_name": "ADC-277", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-277.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7412": {"model_id": "7412", "model_name": "ADC-278", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10239": {"protein_sequence": {"accession": "UTS94223.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNEKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"}, "dna_sequence": {"accession": "ON651470.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATGAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007994", "ARO_id": "46786", "ARO_name": "ADC-278", "CARD_short_name": "ADC-278", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-278.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7413": {"model_id": "7413", "model_name": "ADC-279", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10240": {"protein_sequence": {"accession": "UTS94224.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANFNSQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651471.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACTTCAACTCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007995", "ARO_id": "46787", "ARO_name": "ADC-279", "CARD_short_name": "ADC-279", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-279.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7414": {"model_id": "7414", "model_name": "ADC-280", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10241": {"protein_sequence": {"accession": "UTS94225.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDILSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651472.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATTTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007996", "ARO_id": "46788", "ARO_name": "ADC-280", "CARD_short_name": "ADC-280", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-280.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7415": {"model_id": "7415", "model_name": "ADC-281", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10242": {"protein_sequence": {"accession": "UTS94249.1", "sequence": "MQFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQILEKTIFPDLGLKHSYINVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPADIQRAINETHKGFCQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651496.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCAATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAATTTTAAGCCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTGGGCATTATTCAAAATAACAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAGTACTATTTTTGAGCTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTAATGACACGCCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAATCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATATAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTTAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTGCCAAGTGGGTACGATGTATCAAGCACTAGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "42801", "NCBI_taxonomy_name": "Acinetobacter lactucae", "NCBI_taxonomy_id": "1785128"}}}}, "ARO_accession": "3007997", "ARO_id": "46789", "ARO_name": "ADC-281", "CARD_short_name": "ADC-281", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-281.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7416": {"model_id": "7416", "model_name": "ADC-282", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10243": {"protein_sequence": {"accession": "UTS94250.1", "sequence": "MRFKKISCLLLPPLFIISTSIYAGNTPKEQEVKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQRAISETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "ON651497.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTATTAGTACCTCAATTTATGCGGGCAATACACCAAAAGAACAAGAAGTTAAAAAACTGGTAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCCGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTGATGACACACCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAATCTCGCCTTACAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAATGTACCCAAAACTCAAATGCAAAATTATGCATATGGCTATAACCAAGAAAATCAGCCGATCCGAGTTAACCCTGGCCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAGTGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36787", "NCBI_taxonomy_name": "Acinetobacter pittii", "NCBI_taxonomy_id": "48296"}}}}, "ARO_accession": "3007998", "ARO_id": "46790", "ARO_name": "ADC-282", "CARD_short_name": "ADC-282", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-282.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7417": {"model_id": "7417", "model_name": "ADC-283", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10244": {"protein_sequence": {"accession": "UUM03672.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OP131856.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCTGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3007999", "ARO_id": "46791", "ARO_name": "ADC-283", "CARD_short_name": "ADC-283", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-283.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7418": {"model_id": "7418", "model_name": "ADC-284", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10245": {"protein_sequence": {"accession": "UVU92350.1", "sequence": "MRFKKISCLLLPPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQALEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYMVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"}, "dna_sequence": {"accession": "OP297826.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGCCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATATGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "35507", "NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470"}}}}, "ARO_accession": "3008000", "ARO_id": "46792", "ARO_name": "ADC-284", "CARD_short_name": "ADC-284", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-284.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7419": {"model_id": "7419", "model_name": "ADC-285", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10246": {"protein_sequence": {"accession": "UVU92353.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKNQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQTVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OP297829.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAATCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTACGTAAATGTACCGAAGAACCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAACTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36787", "NCBI_taxonomy_name": "Acinetobacter pittii", "NCBI_taxonomy_id": "48296"}}}}, "ARO_accession": "3008001", "ARO_id": "46793", "ARO_name": "ADC-285", "CARD_short_name": "ADC-285", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-285.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7420": {"model_id": "7420", "model_name": "ADC-286", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10247": {"protein_sequence": {"accession": "UZF98454.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OP745003.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTAATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGTTCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36787", "NCBI_taxonomy_name": "Acinetobacter pittii", "NCBI_taxonomy_id": "48296"}}}}, "ARO_accession": "3008002", "ARO_id": "46794", "ARO_name": "ADC-286", "CARD_short_name": "ADC-286", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-286.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7421": {"model_id": "7421", "model_name": "ADC-287", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10248": {"protein_sequence": {"accession": "UZF98456.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OP745005.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGTTCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36787", "NCBI_taxonomy_name": "Acinetobacter pittii", "NCBI_taxonomy_id": "48296"}}}}, "ARO_accession": "3008003", "ARO_id": "46795", "ARO_name": "ADC-287", "CARD_short_name": "ADC-287", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-287.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7422": {"model_id": "7422", "model_name": "ADC-288", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10249": {"protein_sequence": {"accession": "UZF98458.1", "sequence": "MRFNKISCLLLPPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNNSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLGTYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKIVALSMNKPFDQVLEKTIFPNLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OP745007.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAACAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCTGTTCAAGATAAAAAAGCCGTAAATAATAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCTACAGCAGGTGGATATGCCAAAACAAAAGGGACAATCTCTTTTAAAGACACACCTGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAGGTTAACTTACTTCAACTTGGTACCTATACAAGTGGCAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCTAGTATTGGCCTATTTGGAAAGATTGTAGCTTTGTCTATGAATAAACCTTTTGATCAAGTCTTAGAAAAAACAATTTTTCCAAATCTGAGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCAGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCTCTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATCAAGGCAGCGTATGCGGTGTTAAATGCAATAAAAAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36787", "NCBI_taxonomy_name": "Acinetobacter pittii", "NCBI_taxonomy_id": "48296"}}}}, "ARO_accession": "3008004", "ARO_id": "46796", "ARO_name": "ADC-288", "CARD_short_name": "ADC-288", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-288.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7423": {"model_id": "7423", "model_name": "ADC-289", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10250": {"protein_sequence": {"accession": "UZQ18804.1", "sequence": "MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLTLQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKDNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OP806904.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAGCCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTATTATTCAAAACAATAAAAAATATGAAACGTATTATGGCCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCAACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCACCTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACCAATGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGACAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36949", "NCBI_taxonomy_name": "Acinetobacter nosocomialis", "NCBI_taxonomy_id": "106654"}}}}, "ARO_accession": "3008005", "ARO_id": "46797", "ARO_name": "ADC-289", "CARD_short_name": "ADC-289", "ARO_description": "Extended-spectrum class C beta-lactamase ADC-289.", "ARO_category": {"43920": {"category_aro_accession": "3005460", "category_aro_cvterm_id": "43920", "category_aro_name": "ADC beta-lactamases pending classification for carbapenemase activity", "category_aro_description": "ADC beta-lactamases with undetermined carbapenemase activity.", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "7424": {"model_id": "7424", "model_name": "ADC-290", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"10251": {"protein_sequence": {"accession": "UZQ18805.1", "sequence": "MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"}, "dna_sequence": {"accession": "OP806905.1", "fmin": "0", "fmax": "1152", "strand": "+", "sequence": "ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTAAAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGTGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTACCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCCACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATG