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Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: strict and loose. A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.", "model_param": {"$insert": {"snp": {"param_type": "single resistance variant", "param_value": {"8942": "G45D"}, "clinical": {"8942": "G45D"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}}, "model_type_id": "40293"}}, "1670": {"$update": {"ARO_category": {"$update": {"35996": {"$update": {"category_aro_name": "clavulanic acid"}}}}}}, "2013": {"$update": {"ARO_category": {"$insert": {"37025": {"category_aro_name": "patricin B", "category_aro_cvterm_id": "37025", "category_aro_accession": "3000681", "category_aro_class_name": "Antibiotic", "category_aro_description": "Patricin B is a streptogramin B antibiotic."}}}}}, "2409": {"$update": {"ARO_category": {"$delete": ["37084", "35980", "35981", "36992", "36993", "35995", "36991", "36994", "35990", "35939", "36309", "36982", "36689", "35977", "35975", "37086", "40928", "35976", "35971", "35973", "40944", "35930", "36995", "35934", "40943", "35927", "36989", "36988", "40929", "36981", "36980", "36983", "37085", "36985", "36984", "36987", "36986", "37141", "36979", "36978", "35978", 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{"$delete": ["35940", "36220", "36998", "36999", "36189", "36996", "36997", "35968", "36667", "37001", "35953", "35957", "35956", "35955", "35931", "35922", "35932", "37045", "37044", "36192", "36291", "36353", "35986", "35958", "37036", "37034", "37035", "37011", "37012", "35966", "35949", "35960", "36174", "35969", "35926", "35924", "35943"]}}}, "2142": {"$update": {"ARO_category": {"$delete": ["35940", "36220", "36998", "36999", "36189", "36996", "36997", "35968", "36667", "37001", "35953", "35957", "35956", "35955", "35931", "35922", "35933", "35958", "35935", "37045", "37044", "36291", "36353", "35986", "35932", "37036", "37034", "37035", "37011", "37012", "35966", "35949", "35960", "36174", "35969", "35926", "35924", "35943"]}}}, "2141": {"$update": {"ARO_category": {"$delete": ["35940", "36220", "36998", "36999", "36189", "36996", "36997", "36667", "37001", "35953", "35957", "35956", "35955", "35931", "35922", "35933", "35958", "37045", "37044", "36192", "36291", "36353", 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The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-2 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.", "model_sequences": {"sequence": {"5791": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTTAAAAAAAGTGCAAGTACATTTATTTTTTTGCTCTGCCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATGGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGAATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACCCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGCGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAGCAGTGGCTATAAGCCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTGTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGGAGTACTAAATAA", "fmax": "885", "accession": "LC178555.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter asburiae", "NCBI_taxonomy_id": "61645", "NCBI_taxonomy_cvterm_id": "36926"}, "protein_sequence": {"accession": "BAX00166.1", "sequence": "MFFFKKSASTFIFLLCLPLNSFASQESNGVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAISLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGLYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"}}}}, "ARO_category": {"42915": {"category_aro_name": "FRI beta-lactamase", "category_aro_cvterm_id": "42915", "category_aro_accession": "3004796", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "FRI-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42917", "model_name": "FRI-2", "model_type_id": "40292"}, "3433": {"model_id": "3433", "ARO_accession": "3001722", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-266 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5629": {"dna_sequence": {"partial": "0", "sequence": "ATGCGAAAAAAGTTCAAAGTTGCTCTGCTATGTAGTTCGTTATGCTTAAGTTTAGGCTTGGTTGCTTGTCACAGCTTAAATTCAGAGCTGCAGATTGCAGAACAGCAAAAGCAACAACAAAAAATTTCTAAGCTATTTGTGAATGCCAAAACAGAAGGCGTATTTGTCACTTATGACGGTCAAAAGATACATGAATATGGGAATGCCTTAAATCGAGCTCAAACGTCGTATATCCCTGCATCTACTTTTAAAATGCTCAATGCTTTGATTGGCATCCAACATCATAAAACGACACCCAATGAAGTTTTTAAATGGAATGGAGAAAAGCGCAGATTTAAGAGCTGGGAAAAAGATTTGACCTTAACTGAGGCGATTCAAGCATCCGCTGTTCCTATTTATCAAGAATTAGCCAGACGAATAGGTTTAGATTTGATGGCATCTGAAGTTAAAAGAATAGGTTTTGGAAATTCAGATATAGGCAATCAGGTCGATAATTTTTGGTTGGTTGGCCCATTAAAAATCACACCGATTCAAGAAGTCAGATTTACCTACGCGTTGGCAAATGAGCAATTGGCGTTTGACATTCCTGTTCAGCAGCAAGTTAAGCAAATGTTATTGGTGGATCAGATGAATGGGACAAAAGTTTATGCGAAAAGTGGTTGGGGAATGGATGTTGAGCCACAAGTGGGATGGTGGACAGGATGGGTAGAGCAGCCTAATGGTAAAGTAACTGCATTTTCTCTAAATATGGAGATGAATAAAACTGAACATGTGGAGGCTCGGAAAACGATTGTTTATGAGGCATTGCAGCAGTTAGGTTTAATTTAG", "fmax": "268400", "accession": "APPO01000008.1", "fmin": "267572", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter venetianus RAG-1 = CIP 110063", "NCBI_taxonomy_id": "1191460", "NCBI_taxonomy_cvterm_id": "42796"}, "protein_sequence": {"accession": "ENV38192.1", "sequence": "MRKKFKVALLCSSLCLSLGLVACHSLNSELQIAEQQKQQQKISKLFVNAKTEGVFVTYDGQKIHEYGNALNRAQTSYIPASTFKMLNALIGIQHHKTTPNEVFKWNGEKRRFKSWEKDLTLTEAIQASAVPIYQELARRIGLDLMASEVKRIGFGNSDIGNQVDNFWLVGPLKITPIQEVRFTYALANEQLAFDIPVQQQVKQMLLVDQMNGTKVYAKSGWGMDVEPQVGWWTGWVEQPNGKVTAFSLNMEMNKTEHVEARKTIVYEALQQLGLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-266", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38122", "model_name": "OXA-266", "model_type_id": "40292"}, "3498": {"model_id": "3498", "ARO_accession": "3001605", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-414 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5693": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ584914.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07401.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-414", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38005", "model_name": "OXA-414", "model_type_id": "40292"}, "3499": {"model_id": "3499", "ARO_accession": "3001607", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-416 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5694": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATTTAATCACCGCGATGAAATATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTGCACGCCTTCGATTATGGCAATGAGGACATTTCGGGCAATTTAGATACTTTTTGGCTTGATGGTGGCATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATCGTTAAACAAGCCATGCTTACTGAGGCGAATGCTGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAGCTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG", "fmax": "798", "accession": "KP264119.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Shewanella xiamenensis", "NCBI_taxonomy_id": "332186", "NCBI_taxonomy_cvterm_id": "39674"}, "protein_sequence": {"accession": "AKH90740.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDTFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-416", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38007", "model_name": "OXA-416", "model_type_id": "40292"}, "3496": {"model_id": "3496", "ARO_accession": "3001603", "model_param": {"blastp_bit_score": {"param_value": "566", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-412 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5691": {"dna_sequence": {"partial": "0", "sequence": "ATGAACGTTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ584921.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07407.1", "sequence": "MNVKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-412", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38003", "model_name": "OXA-412", "model_type_id": "40292"}, "3497": {"model_id": "3497", "ARO_accession": "3001604", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-413 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5692": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ584922.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07408.1", "sequence": "MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-413", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38004", "model_name": "OXA-413", "model_type_id": "40292"}, "3494": {"model_id": "3494", "ARO_accession": "3001600", "model_param": {"blastp_bit_score": {"param_value": "565", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-409 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5689": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAAAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "828", "accession": "KJ584918.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07405.1", "sequence": "MNIKALLLITSAIFISACCSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEKKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-409", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38000", "model_name": "OXA-409", "model_type_id": "40292"}, "3495": {"model_id": "3495", "ARO_accession": "3001602", "model_param": {"blastp_bit_score": {"param_value": "566", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-411 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5690": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ584920.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07406.1", "sequence": "MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-411", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38002", "model_name": "OXA-411", "model_type_id": "40292"}, "3492": {"model_id": "3492", "ARO_accession": "3001598", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-407 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5687": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTACTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTGAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCACCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ584916.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07403.1", "sequence": "MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIHQGQTQQSYGNDLTRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSEEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFTLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-407", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37998", "model_name": "OXA-407", "model_type_id": "40292"}, "3493": {"model_id": "3493", "ARO_accession": "3001599", "model_param": {"blastp_bit_score": {"param_value": "566", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-408 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5688": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTCAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ584917.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07404.1", "sequence": "MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-408", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37999", "model_name": "OXA-408", "model_type_id": "40292"}, "3490": {"model_id": "3490", "ARO_accession": "3001596", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-405 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5685": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG", "fmax": "786", "accession": "KM589641.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia marcescens", "NCBI_taxonomy_id": "615", "NCBI_taxonomy_cvterm_id": "36783"}, "protein_sequence": {"accession": "AJA30430.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-405", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37996", "model_name": "OXA-405", "model_type_id": "40292"}, "3491": {"model_id": "3491", "ARO_accession": "3001597", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-406 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5686": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGTATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ584915.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJD07402.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-406", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37997", "model_name": "OXA-406", "model_type_id": "40292"}, "3416": {"model_id": "3416", "ARO_accession": "3001457", "model_param": {"blastp_bit_score": {"param_value": "570", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-152 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5611": {"dna_sequence": {"partial": "0", "sequence": "ATGAATACGATAATCTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCGGTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAAGCCGCGCCGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCGCCGCGGAGGGCGTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCCGCACGTGCCGGGAAGCGCATGTCGCCGGCGTCGACTTACAAGATATTCAACAGCCTGCTGGCGCTCGACTCCGGGGCGCTGGACAACGAACGTGCGATCATTCCCTGGGATGGCAAGCCGCGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGCCTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCAGTACGCGCAGGCGAAGCTGAACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGACGACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCGTGCAGCGTCTCGCGCGTGGCACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCCACGCCGGACTATGTGCTTCACGGCAAGACGGGCTGGTTCGTCGACAAGAAGCCCGATATCGGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCACCAGCGTCGCGATCAACATCGACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGGCGGTGCTGAAGGACCTGAAGCTGATCTGA", "fmax": "861", "accession": "KP771980.1", "fmin": "3", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea pnomenusa", "NCBI_taxonomy_id": "93220", "NCBI_taxonomy_cvterm_id": "36932"}, "protein_sequence": {"accession": "ALA99186.1", "sequence": "MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAAPGRITERADWGKLFAAEGVKGTIVVLDARTQTYQAYDAARAGKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRQYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFVQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVAINIDMLSEADAPKRARIVKAVLKDLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-152", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37857", "model_name": "OXA-152", "model_type_id": "40292"}, "3417": {"model_id": "3417", "ARO_accession": "3001458", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-153 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5612": {"dna_sequence": {"partial": "0", "sequence": "TCAGATCAACTGCAAACTACTGAGCACGGCACGAACGATACGGGCGCGCTTGGGCGCATCGGCATCGTCCTTCAGATCGATGTTCAACGCTACGCTCGTGATGTTGCCGTCGCGCTCAATCCAGCCCACCCACCAGCCGATGTCCGGCTTCTTGTCGACGAACCAGCCCGTCTTGCCATGCAACACGTAATCAGGATTGGCCTCGACAATCGAAATCTGACGCACGATGTCTTGCGAGCGTGCAGAGAACGGTAACGTCCCTCGCGCGAGACGTTGCAGGAAATCGACCTGCTCGCGTGCCGAGATCTGCAAGCTGTCGTCGACCCAGTAGGCGTCTGCGGCACGACCGATAGTGTGGTTCCCATACCCGGCCTCATTGAGTTTGCTCTGTGCAAACTGACGCGCAATCTTGTGCGAGACCACCTGATAGCACGGCAAACACGACACGCGAAACGCCGTGCGCAGATCCATCGCCGCGTTCCAGTACTTCCCGCGTCGCGGCTTGCCGTCCCAGGGAATGATCTCGCGTTCGTTATCGAGGGCGCCCGACTCGAGCGCCAGCAGGCTGTTGAAGATCTTGTACGTCGATGCAGGCGACATCCGCCGCTCGGCGCGCGCCGTGTCGAACGCCTGATACGTTTGCGTGCGTCCGTCGAGCACCACGATCGTTCCCTTAACACCTTCCGCATCGAAGAACTTGCCCCAATCGGCACGCTCCTTCATGTGCACCGCAGCGGCCTTAGTCCCCGCGGCCCCGCCCGCCGCTTCCGTCGCATGCGCCGGAACGGCGAACACCATGGGAGACACGACCGCGAGCGCAACCCGCAGCCCGAAGACACCACGCCGCCAGCGAGAAATTATCTTTTTCAT", "fmax": "24671", "accession": "CEWL01000009.1", "fmin": "23801", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea apista", "NCBI_taxonomy_id": "93218", "NCBI_taxonomy_cvterm_id": "42785"}, "protein_sequence": {"accession": "CFB60580.1", "sequence": "MKKIISRWRRGVFGLRVALAVVSPMVFAVPAHATEAAGGAAGTKAAAVHMKERADWGKFFDAEGVKGTIVVLDGRTQTYQAFDTARAERRMSPASTYKIFNSLLALESGALDNEREIIPWDGKPRRGKYWNAAMDLRTAFRVSCLPCYQVVSHKIARQFAQSKLNEAGYGNHTIGRAADAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVALNIDLKDDADAPKRARIVRAVLSSLQLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-153", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37858", "model_name": "OXA-153", "model_type_id": "40292"}, "3414": {"model_id": "3414", "ARO_accession": "3001450", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-135 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5609": {"dna_sequence": {"partial": "0", "sequence": "TCAGATCAGCTTCAGGTCCTTCAGCACCGACTTCACGATGCGTGCCCGTTTCGGGGCGTCCGCCTCCGACAGCATGTCGATGTTGATCGCGACGCTGGCGATGTTGCCGTCGCGCTCGATCCACCCTACCCACCAGCCGATATCGGGCTTCTTGTCGACGAACCAGCCCGTCTTGCCGTGAAGCACATAGTCCGGCGTGGCTTCGACGATCGACATCTGGCGCACGATGTCCTGCGAGCGCGCAGAGAACGGCAACGTGCCACGCGCGAGACGCTGCAGGAAGTCCACCTGCTCACGCGCCGAAATCTGCAGACTGTCGTCGACCCAATAGGCGTCCGGCGCGCCGCCAATGGTGCGGTTGCCATACCCGACCTCGTTCAGCTTCGCCTGCGCGTACCGGCGCCCGATCTTGTGCGAGACGACCTGATAGCAGGGCAGGCATGACACGCGAAACGCGGTCCTCAGGTCCATCGCCGCGTTCCAGTTCTTGATGCGTCGCGGCTTGCCATCCCAGGGAATGATCGCGCGTTCGTTGTCCAGCGCCCCGGAGTCGAGCGCCAGCAGGCTGTTGAATATCTTGTAAGTCGACGCCGGCGACATGCGCTTCTCGGCACGTGCGGCGTCGTAGGCCTGATAGGTTTGCGTGCGTGCGTCGAGCACCACGATCGTGCCCTTCACGCCCTCCGCGGTGAACAGCTTGCCCCAGTCGGCGCGCTCGGTGATGCGCCCCGGCGCGGCTTTCGGCACGTCGGCCGCATAGGCCGCAGGGGTGGCGGCGAGCGTTGCGGGCAAGACGACCGCGCCGACCAGCCGCCGCCACAGGCCGGCACGCCACCGGCGAGAAATTATCGTATTCAT", "fmax": "1910080", "accession": "UGSG01000001.1", "fmin": "1909222", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea pnomenusa", "NCBI_taxonomy_id": "93220", "NCBI_taxonomy_cvterm_id": "36932"}, "protein_sequence": {"accession": "SUA76968.1", "sequence": "MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAAPGRITERADWGKLFTAEGVKGTIVVLDARTQTYQAYDAARAEKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRRYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNIASVAINIDMLSEADAPKRARIVKSVLKDLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-135", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37850", "model_name": "OXA-135", "model_type_id": "40292"}, "3415": {"model_id": "3415", "ARO_accession": "3001456", "model_param": {"blastp_bit_score": {"param_value": "570", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-151 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5610": {"dna_sequence": {"partial": "0", "sequence": "TCAGATCAGCTTCAGGTCCTTCAGCACCGACTTCACGATGCGTGCCCGTTTCGGGGCGTCCGCCTCCGACAGCATGTCGATGTTGATCGCGACGCTGGCGATGTTGCCGTCGCGCTCGATCCACCCTACCCACCAGCCGATATCGGGCTTCTTGTCGACGAACCAGCCCGTCTTGCCGTGAAGCACATAGTCCGGCGTGGCTTCGACGATCGACATCTGGCGCACGATGTCCTGCGAGCGCGCAGAGAACGGCAACGTGCCACGCGCGAGACGCTGCAGGAAGTCCACCTGCTCACGCGCCGAAATCTGCAGACTGTCGTCGACCCAATAGGCGTCCGGCGCGCCGCCAATGGTGCGGTTGCCATACCCGACCTCGTTCAGCTTCGCCTGCGCGTACCGGCGCCCGATCTTGTGCGAGACGACCTGATAGCAGGGCAGGCATGACACGCGAAACGCGGTCCTCAGGTCCATCGCCGCGTTCCAGTTCTTGATGCGTCGCGGCTTGCCATCCCAGGGAATGATCGCGCGTTCGTTGTCCAGCGCCCCGGAGTCGAGCGCCAGCAGGCTGTTGAATATCTTGTAAGTCGACGCCGGCGACATGCGCTTCTCGGCACGTGCGGCGTCGTAGGCCTGATAGGTTTGCGTGCGTGCGTCGAGCACCACGATCGTGCCCTTCACGCCCTCCGCGGTGAACAGCTTGCCCCAGTCGGCGCGCTCGGTGATGCGCCCCGGCGCGGCTTTCGGCACGTCGGCCGCATAGGCCGCAGGGGTGGCGGCGAGCGTTGCGGGCAAGACGACCGCGCCGACCAGCCGCCGCCACAGGCCGGCACGCCACCGGCGAGAAATTATCGTATTCAT", "fmax": "1910080", "accession": "UGSG01000001.1", "fmin": "1909222", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea pnomenusa", "NCBI_taxonomy_id": "93220", "NCBI_taxonomy_cvterm_id": "36932"}, "protein_sequence": {"accession": "SUA76968.1", "sequence": "MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAAPGRITERADWGKLFTAEGVKGTIVVLDARTQTYQAYDAARAEKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRRYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNIASVAINIDMLSEADAPKRARIVKSVLKDLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-151", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37856", "model_name": "OXA-151", "model_type_id": "40292"}, "3412": {"model_id": "3412", "ARO_accession": "3001448", "model_param": {"blastp_bit_score": {"param_value": "566", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-126 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5607": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGATGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "EU255295.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ABX45065.1", "sequence": "MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLMGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-126", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37848", "model_name": "OXA-126", "model_type_id": "40292"}, "3413": {"model_id": "3413", "ARO_accession": "3001449", "model_param": {"blastp_bit_score": {"param_value": "565", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-127 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5608": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCAGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "EU255296.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ABX45066.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWQVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-127", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37849", "model_name": "OXA-127", "model_type_id": "40292"}, "3410": {"model_id": "3410", "ARO_accession": "3001446", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-124 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5605": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCACATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "EU255293.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ABX45063.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNAHIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-124", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37846", "model_name": "OXA-124", "model_type_id": "40292"}, "3411": {"model_id": "3411", "ARO_accession": "3001447", "model_param": {"blastp_bit_score": {"param_value": "567", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-125 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5606": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCGGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATAGCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "EU255294.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ABX45064.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVRPQGNIVAFSLNLEMKKGIASSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-125", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37847", "model_name": "OXA-125", "model_type_id": "40292"}, "3418": {"model_id": "3418", "ARO_accession": "3001459", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-154 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5613": {"dna_sequence": {"partial": "0", "sequence": "ATGAAACGAATTCTCTCTCACTGGTGTCGCGCGGCTGTCGTGCTGCGTCTGGCGTCGGCGGTCGTCGCGCATGGTCTGCTGCCCTCGCCAGCACACGCGCTGGAATTGTCGCGCGCGTCAGCCGCGGCAGCACCTTCCGTGGCAGCGCCCGTCCACGTGACCGAGCGTGCCGACTGGGGCAAGTTCTTTGCGGCGGAAAACGTGAAGGGCACGGTCGTCGTGCTCGACGGCAAGACACAGACGTATCAGGCGTACGACTCGGCGCGCGCCGAGCGGCGCATGTCCCCGGCGTCGACGTACAAGATTTTCAACAGTCTGCTGGCGCTGGAATCGGGTGCGCTGGACAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCGCGCCGGATTAAGGCGTGGAATGCAGAATTGAATCTGCGCGACGCGTTTCGCGTGTCTTGCTACCCGTGCTATCAGGTCGTTTCGCACAAGATTCCGCGTGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGGACCATCGGTCGGGTGAACGACACCTATTGGGTGGACGACAGTTTGCAGATCTCAGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCGCGTGGCACGTTGCCGTTCTCCGCGCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACGCCGACTATGTGCTGCACGGCAAGACCGGCTGGTTCGTCGACAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTGGAGCGTGACGGCAATCTGACGATGATCGCGCTGAACATCGACATGAACGGCGACGCCGACGGCCCGAAGCGCGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTGA", "fmax": "4450450", "accession": "LT906435.1", "fmin": "4449571", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea sputorum", "NCBI_taxonomy_id": "93222", "NCBI_taxonomy_cvterm_id": "42786"}, "protein_sequence": {"accession": "SNU87672.1", "sequence": "MKRILSHWCRAAVVLRLASAVVAHGLLPSPAHALELSRASAAAAPSVAAPVHVTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALDNERETIPWDGKPRRIKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANADYVLHGKTGWFVDKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-154", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37859", "model_name": "OXA-154", "model_type_id": "40292"}, "3419": {"model_id": "3419", "ARO_accession": "3001460", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-155 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5614": {"dna_sequence": {"partial": "0", "sequence": "ATGAAACGAATTCTCTCTCGCTGGCGTCGCGCGGCTGTCGTGCTGCGTCTGGCGTCGGCGGTCGTCGCGCATGGTCTGCTGCCCTCGCCAGCACACGCGCTGGAATTGTCGCGGGCGTCAGCCGCGGCGGCACCTTCCGTGGCAGCGCCCGTCCACGTGACCGAGCGTGCCGACTGGGGCAAGTTCTTTGCGGCGGAAAACGTGAAGGGCACGGTCGTCGTGCTCGACGGCAAGACACAGACGTATCAGGCGTACGACTCGGCGCGCGCCGAGCGGCGCATGTCCCCGGCGTCGACGTACAAGATATTCAACAGTCTGCTGGCGCTGGAATCGGGTGCGCTGGACAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCGCGCCGGATTAAGGCGTGGAATGCAGAATTGAATCTGCGTGACGCGTTTCGTGTGTCTTGCTACCCGTGCTATCAGGTCGTTTCGCACAAGATTCCGCGTGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGGACCATCGGTCGGGTGAACGACACCTATTGGGTGGACGACAGTTTGCAGATCTCGGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCGCGTGGCACGTTGCCGTTCTCCGCGCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACGCCGACTATGTGCTGCACGGCAAGACCGGCTGGTTCGTCGAGAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTGGAGCGTGACGGCAATCTGACGATGATCGCGCTGAACATCGACATGAACGGCGACGCCGACGGCCCGAAGCGTGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTGA", "fmax": "1048", "accession": "KP771983.1", "fmin": "169", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea sputorum", "NCBI_taxonomy_id": "93222", "NCBI_taxonomy_cvterm_id": "42786"}, "protein_sequence": {"accession": "ALA99189.1", "sequence": "MKRILSRWRRAAVVLRLASAVVAHGLLPSPAHALELSRASAAAAPSVAAPVHVTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALDNERETIPWDGKPRRIKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANADYVLHGKTGWFVEKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-155", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37860", "model_name": "OXA-155", "model_type_id": "40292"}, "3557": {"model_id": "3557", "ARO_accession": "3004745", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "AZECL-25 is a class C beta-lactamase that is found in Enterobacter cloacae.", "model_sequences": {"sequence": {"5752": {"dna_sequence": {"partial": "0", "sequence": "ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTTCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA", "fmax": "1146", "accession": "KJ949106.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "AIG20028.1", "sequence": "MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQASSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42855": {"category_aro_name": "AZECL Beta-lactamase", "category_aro_cvterm_id": "42855", "category_aro_accession": "3004744", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "AZECL is a beta-lactamase under the class C beta-lactamases."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "AZECL-25", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42856", "model_name": "AZECL-25", "model_type_id": "40292"}, "3555": {"model_id": "3555", "ARO_accession": "3004740", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "AST-1 is a broad-spectrum beta-lactamase gene found in Nocardia asteroides.", "model_sequences": {"sequence": {"5750": {"dna_sequence": {"partial": "0", "sequence": "GTGACTTTCTCCGCTCTCCCCTTCCGCCGGGCCGACCGCCGGCGCCTGCTCGCCGCCGCGCTCGCGGCCTGCGCACTGACCCTGACGGCGGCCTGTGATTCCGGCACCGTCACCGTTCCGGTGACGGACTCGGTGACCACCTCGGCGGTGGCCGATCCCCGGTTCGCCGAACTGGAAACCACTTCCGGCGCCCGGCTGGGCGTGTTCGCCGTCGACACCGGCTCCGGGCGCACCGTCGCCCACCGCGCCGACGAACGGTTCCCGATGGCGTCCACGTTCAAGGGCCTGGCGTGCGGGGCGCTGCTGCGCGAGCATCCCCTGTCGACGGGCTACTTCGATCAGGTGATCCACTACTCCGCCGCCGAGCTGGTCGAGTATTCGCCGGTGACCGAGACCCGGGTCGAGACCGGCATGACGGTCCGGGAACTGTGCGACGCCGCGATCACGGTTTCCGACAACACGGCGGGCAATCAGTTGCTGAAACTGCTCGGTGGACCGGAGGGATTCACCGCGTCCCTGCGTTCCCTCGGCGACGCCACGTCGCGGCTGGACCGCTGGGAGACCGACCTGAACACCGCGATTCCCGGGGATGAGCGCGATACCACCACCCCGGCCGCGCTCGCCGCCGACTACCGCGCGCTCGTCGTCGGCGATGTCCTCGGCGCACCCGAACGCGACCAGCTGAAGGCATGGCTCGTCGCCAACACCACCGGTGCCACCCGGATTCGCGCGGGTCTGCCCGCGGACTGGACCGTCGGCGACAAGACCGGCAGCCCGGCCTACGGTTCGGCCCTCGATGTCGCGGTGGCCTGGCCGCCCGGTCGCGCGCCGATCGTCATCGCGGTGCTGTCGACTAAGTCCGAGCAGGACGCCGAACCCGACAACGCCCTGCTCGCCGAGGCCACCCGCGTGGTGGTCGACGCGCTCGGATAG", "fmax": "1092", "accession": "AF279904.1", "fmin": "159", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Nocardia asteroides", "NCBI_taxonomy_id": "1824", "NCBI_taxonomy_cvterm_id": "42852"}, "protein_sequence": {"accession": "AAG44836.1", "sequence": "MTFSALPFRRADRRRLLAAALAACALTLTAACDSGTVTVPVTDSVTTSAVADPRFAELETTSGARLGVFAVDTGSGRTVAHRADERFPMASTFKGLACGALLREHPLSTGYFDQVIHYSAAELVEYSPVTETRVETGMTVRELCDAAITVSDNTAGNQLLKLLGGPEGFTASLRSLGDATSRLDRWETDLNTAIPGDERDTTTPAALAADYRALVVGDVLGAPERDQLKAWLVANTTGATRIRAGLPADWTVGDKTGSPAYGSALDVAVAWPPGRAPIVIAVLSTKSEQDAEPDNALLAEATRVVVDALG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "42851": {"category_aro_name": "AST Beta-lactamase", "category_aro_cvterm_id": "42851", "category_aro_accession": "3004741", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A family of beta-lactamase known for their broad spectrum resistance profile."}}, "ARO_name": "AST-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42850", "model_name": "AST-1", "model_type_id": "40292"}, "3554": {"model_id": "3554", "ARO_accession": "3004739", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ARL-6 is a beta-lactamase gene found in Staphylococcus arlettae.", "model_sequences": {"sequence": {"5749": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACTTTTAAAGCCATTACGAGTGGGTTATTATTACAGCAAAATTCTCCTGAAGCATTAAACAAAACTGTAACAATAAAAGAATCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAACAACTCGGTGGTCTGGATCAGCTTTCGTCTCGCTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTATGAACCCGAATTAAATAACTATGATCCACAAAGTACGGCAGATACATCAACACCTCGTGCTACTGCCCATAATTTGCAAAATCTATTAACAACAGATGCCGTTGCACCACAACAGCGTAAGTTTTTACAAAATTTAATGTTGAACAATAAAACAGGTGAGAGTTTAATCAAAAAAGGTGTCCCTAACAGTTATAAAGTAGGTGACAAAAGTGGCCAAGGTACAACTTATGGCACGCGTAATGATGTTGCCGTCATCTATCCAAAACATCAAACAAAACCAATTATTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA", "fmax": "3085", "accession": "KY464892.1", "fmin": "2236", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus arlettae", "NCBI_taxonomy_id": "29378", "NCBI_taxonomy_cvterm_id": "42844"}, "protein_sequence": {"accession": "APY23865.1", "sequence": "MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQNSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQLSSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHNLQNLLTTDAVAPQQRKFLQNLMLNNKTGESLIKKGVPNSYKVGDKSGQGTTYGTRNDVAVIYPKHQTKPIILVVFTKHQQQDAQPQDELVAQAARHAIHQLD"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42853": {"category_aro_name": "ARL Beta-lactamase", "category_aro_cvterm_id": "42853", "category_aro_accession": "3004742", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae."}}, "ARO_name": "ARL-6", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42849", "model_name": "ARL-6", "model_type_id": "40292"}, "3553": {"model_id": "3553", "ARO_accession": "3004738", "model_param": {"blastp_bit_score": {"param_value": "570", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ARL-5 is a beta-lactamase gene found in Staphylococcus arlettae.", "model_sequences": {"sequence": {"5748": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAATTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTTGCTTACACAACTGCTAGTGCTTCAGCGCAAGATTTAACAAAATTGGAACATAAGAATGATGCCACAGTTGGTGTTTATGGTATTAATACTGCTACCGGAAAAACTTACTCACACAATGCTGACACACGTTTTGCTTATGCATCAACATTTAAAGCCATTACAAGTGGTTTATTATTACAACAAAGTTCTCCTGAAGCATTAAACAAGACTGTCACTATAAAAGAGTCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATGTCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCAACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTTGTCTTTACCAAACACAAGCAACAAGACGCAAAGCCACAAGATGCGCTTGTAGCACAAGCAGCACGTCAGGCTATACAGCAGCTCGATTAA", "fmax": "3086", "accession": "KY363214.1", "fmin": "2237", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus arlettae", "NCBI_taxonomy_id": "29378", "NCBI_taxonomy_cvterm_id": "42844"}, "protein_sequence": {"accession": "APY23862.1", "sequence": "MKKFFTIFVLLCVCFAYTTASASAQDLTKLEHKNDATVGVYGINTATGKTYSHNADTRFAYASTFKAITSGLLLQQSSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNVIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHKQQDAKPQDALVAQAARQAIQQLD"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42853": {"category_aro_name": "ARL Beta-lactamase", "category_aro_cvterm_id": "42853", "category_aro_accession": "3004742", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae."}}, "ARO_name": "ARL-5", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42848", "model_name": "ARL-5", "model_type_id": "40292"}, "3552": {"model_id": "3552", "ARO_accession": "3004737", "model_param": {"blastp_bit_score": {"param_value": "581", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ARL-4 is a beta-lactamase gene found in Staphylococcus arlettae.", "model_sequences": {"sequence": {"5747": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGTATTAATACTGCTACCGGAAAAACTTACTCACACAATGCTGACACACGTTTTGCTTATGCATCAACATTTAAAGCCATTACAAGTGGTTTATTATTACAACAAAGTTCTCCTGAAGCATTAAACAAGACTGTCACTATAAAAGAGTCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCTACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA", "fmax": "3085", "accession": "KY363206.1", "fmin": "2236", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus arlettae", "NCBI_taxonomy_id": "29378", "NCBI_taxonomy_cvterm_id": "42844"}, "protein_sequence": {"accession": "APY23838.1", "sequence": "MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGKTYSHNADTRFAYASTFKAITSGLLLQQSSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHQQQDAQPQDELVAQAARHAIHQLD"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42853": {"category_aro_name": "ARL Beta-lactamase", "category_aro_cvterm_id": "42853", "category_aro_accession": "3004742", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae."}}, "ARO_name": "ARL-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42847", "model_name": "ARL-4", "model_type_id": "40292"}, "3551": {"model_id": "3551", "ARO_accession": "3004736", "model_param": {"blastp_bit_score": {"param_value": "580", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ARL-3 is a beta-lactamase gene found in Staphylococcus arlettae.", "model_sequences": {"sequence": {"5746": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACATTTAAAGCCATTACAAGTGGGTTATTATTACAACAAAGTTCTCCTGAAGCATTAAACAAGACTGTCACTATAAAAGAGTCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCTACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA", "fmax": "3085", "accession": "KY363208.1", "fmin": "2236", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus arlettae", "NCBI_taxonomy_id": "29378", "NCBI_taxonomy_cvterm_id": "42844"}, "protein_sequence": {"accession": "APY23844.1", "sequence": "MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQSSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHQQQDAQPQDELVAQAARHAIHQLD"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42853": {"category_aro_name": "ARL Beta-lactamase", "category_aro_cvterm_id": "42853", "category_aro_accession": "3004742", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae."}}, "ARO_name": "ARL-3", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42846", "model_name": "ARL-3", "model_type_id": "40292"}, "3550": {"model_id": "3550", "ARO_accession": "3004735", "model_param": {"blastp_bit_score": {"param_value": "580", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ARL-2 is a beta-lactamase gene found in Staphylococcus Arlettae.", "model_sequences": {"sequence": {"5745": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACTTTTAAAGCCATTACGAGTGGGTTATTATTACAGCAAAATTCTCCTGAAGCATTAAACAAAACTGTAACAATAAAAGAATCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCTACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA", "fmax": "3085", "accession": "KY363207.1", "fmin": "2236", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus arlettae", "NCBI_taxonomy_id": "29378", "NCBI_taxonomy_cvterm_id": "42844"}, "protein_sequence": {"accession": "APY23841.1", "sequence": "MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQNSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHQQQDAQPQDELVAQAARHAIHQLD"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42853": {"category_aro_name": "ARL Beta-lactamase", "category_aro_cvterm_id": "42853", "category_aro_accession": "3004742", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae."}}, "ARO_name": "ARL-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42845", "model_name": "ARL-2", "model_type_id": "40292"}, "3559": {"model_id": "3559", "ARO_accession": "3004749", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BCL-1 is a class A beta-lactamase found in Bacillus clausii.", "model_sequences": {"sequence": {"5754": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAGGAGTTTTTTTATGCTGAAAACAAAAATCACGTCGTCTATCCTTGTAGGTGCCTGTTTACTGATTGGTTGTTCGAATGGCAATGAGCAACCGGTTTCCAACGAACCTGAACCTGAAGAGTCTGTCGAGACGGGAGAGGCGGTTTTTAAAGCGTTAGAAGAAGAGTACGCTGCCCGCCTTGGCGTATTTGCTTTAGACACCGGGACAGGACAAACCGTTTCCTACCGCTCCGATGAACGCTTCACCTATGCGTCTGCCCATAAACCACTTGCCGTTGCCGTTCTGCTTCAACAAAAATCAATCGAAGAGTTGGAACAATTGATTACGTACTCGGCCGATGATTTAGTAAACTACAATCCAATTACCGAAAACCACGTTGAGACAGGCATGACACTAAGAGAGTTAAGCGATGCTTCGATTCGTTATAGCGATAACACGGCTGCAAACTTCATTTTCGATGAAATTGGAGGGCCAGAGGGCTTTAAAGAAGGACTTCGAGCGATTGGAGACACGGTAACCGAACCTGAACGAATCGAACCTGAGCTCAATCATGTTGAACCTGGAGAGATCCAAGATACGAGTACACCAGAGGCGTTGGCCAAAAGCTTGCAAGAATTTGCTTTAGGAGAGGCGCTGCCAGCTGACAAACAGGAACTGTTAATCGATTGGCTAATAGGAAACACGACTGGAGATGCTTTAATACGTGCTGGGGTGCCGGAAGGTTGGGAAGTTGGCGACAAAACAGGCGCAGGTTCCTATGGGACTCGAAATGATATTGCCATTCTTTGGCCACCTGAAAAAGAGCCCATTATTTTAGCCGTCCTATCGAGCAAAGACGAAAAGGATGCCGAATATGATGATGAACTGATCGCGAAAGCGACAGAGGAAGTGATCAATCTCCTCGCCCAAACAGAATAG", "fmax": "4236", "accession": "EF540343.1", "fmin": "3312", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bacillus clausii", "NCBI_taxonomy_id": "79880", "NCBI_taxonomy_cvterm_id": "36882"}, "protein_sequence": {"accession": "ABU39980.1", "sequence": "MKRSFFMLKTKITSSILVGACLLIGCSNGNEQPVSNEPEPEESVETGEAVFKALEEEYAARLGVFALDTGTGQTVSYRSDERFTYASAHKPLAVAVLLQQKSIEELEQLITYSADDLVNYNPITENHVETGMTLRELSDASIRYSDNTAANFIFDEIGGPEGFKEGLRAIGDTVTEPERIEPELNHVEPGEIQDTSTPEALAKSLQEFALGEALPADKQELLIDWLIGNTTGDALIRAGVPEGWEVGDKTGAGSYGTRNDIAILWPPEKEPIILAVLSSKDEKDAEYDDELIAKATEEVINLLAQTE"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42860": {"category_aro_name": "BCL Beta-lactamase", "category_aro_cvterm_id": "42860", "category_aro_accession": "3004748", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BCL beta-lactamase is a class A beta-lactamase."}}, "ARO_name": "BCL-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42861", "model_name": "BCL-1", "model_type_id": "40292"}, "3558": {"model_id": "3558", "ARO_accession": "3004747", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BAT-1 is a class D beta-lactamase found in Bacillus atrophaeus.", "model_sequences": {"sequence": {"5753": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAACGCAAGATGCCAGCAGTTTTCTTAGCATTGATCGGTGCAGCCGGTCTATTATTTACTACAAGTGTACAGCCAATAAGCGAAGCTAGTGCTGCCGAAAAGAATCTGAATATCAAAAAGCTCGATGTCGATGAATTTTTTGCCGATCATAACGGAACGTTTATATTACGTGATATGAATAAAGGCAAAACATTTATCTATAATCATGAACGCGCCAACCAAAGATTTGCACCGCAATCGACTTTTAAAGTTCCTAATGCACTCATTGGCTTACAAGTAGGAGCTGTAGAAGATGAATATTCCATTAAATATTGGGATGGCGTGAAGCGGGAAATTGACATCTGGAATCAAGATCACACGCTTGGGTCTGGGATGAGGCATTCAGTTGTTTGGTATTATCAAGCGATGGCCCGTGACATTGGAGAAAGTCGAATGAAGGAATGGATCGAAAAAATTTCCTATGGCAACCAAGATATAAGCGGTGGAATTGACCAGTTTTGGTTAAGCAGCACACTCAAAATTTCTCCGATAGAACAAGCAGACTTTATGGAAAGATTGTATAAAGAGAACCTGCCTTTTGATAAGGATGTCATGAAAACAGTAAAACGGATGATGATTCAGGAGGAAGAAGATCACTCTACTCTTTACGGAAAAACAGGTTCAGGGACAGGCATAGGGTGGTTTTTCGGTTTTGTGAAAATAGACAATCGAGCGTATAGTTTTGTTACGAATATTGATGGAACAGGTGCAGAAGCTAAAAACATCACAATGGATATTTTAAAGAAATATAAGTTATATTAA", "fmax": "18410", "accession": "AJRJ01000061.1", "fmin": "17603", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bacillus atrophaeus C89", "NCBI_taxonomy_id": "334727", "NCBI_taxonomy_cvterm_id": "42859"}, "protein_sequence": {"accession": "EIM09515.1", "sequence": "MKKRKMPAVFLALIGAAGLLFTTSVQPISEASAAEKNLNIKKLDVDEFFADHNGTFILRDMNKGKTFIYNHERANQRFAPQSTFKVPNALIGLQVGAVEDEYSIKYWDGVKREIDIWNQDHTLGSGMRHSVVWYYQAMARDIGESRMKEWIEKISYGNQDISGGIDQFWLSSTLKISPIEQADFMERLYKENLPFDKDVMKTVKRMMIQEEEDHSTLYGKTGSGTGIGWFFGFVKIDNRAYSFVTNIDGTGAEAKNITMDILKKYKLY"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42857": {"category_aro_name": "BAT Beta-lactamase", "category_aro_cvterm_id": "42857", "category_aro_accession": "3004746", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BAT is a class D beta-lactamase."}}, "ARO_name": "BAT-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42858", "model_name": "BAT-1", "model_type_id": "40292"}, "3547": {"model_id": "3547", "ARO_accession": "3003643", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5742": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA", "fmax": "6224407", "accession": "CP038661.1", "fmin": "6223618", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "QBY97442.1", "sequence": "MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-486", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40253", "model_name": "OXA-486", "model_type_id": "40292"}, "3489": {"model_id": "3489", "ARO_accession": "3001595", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-404 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5684": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTCTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCACCTCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ920338.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AIM47096.1", "sequence": "MNIKTLLLITSAILISACSPYIVTANPPHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-404", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37995", "model_name": "OXA-404", "model_type_id": "40292"}, "3488": {"model_id": "3488", "ARO_accession": "3001589", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-403 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5683": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCACATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ920337.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AIM47095.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPHHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-403", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37989", "model_name": "OXA-403", "model_type_id": "40292"}, "3481": {"model_id": "3481", "ARO_accession": "3001551", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-364 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5675": {"dna_sequence": {"partial": "0", "sequence": "ATGCCCCTCCGACTCCCTCTGCGCGCCCTGGGCGCGGCCCTGTCCCTGTTCGCGCTGGCCGGCGCCCCCGCCAGCGCGGCGGTTTTGTGCACCGTGGTGGCCGACGCGGCCGACGGCCGCATCGTGTTCCAGCAAGGCACGCAGGCGGCCTGCGCCGAGCGCTACACGCCCGCCTCGACCTTCAAGCTGCCGATCGCGCTGATGGGCGCGGACGCGGGCATCCTGCAAGGCGCGCACGCGCCAGTCTGGAACTACCAGCCGGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCGACGGACCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTACTCACAACTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACGCCTCGGCCTTCCAGTACGGCAACGAGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCCTGGACGGCGCGTGGATCAACTCGTCGCTGCGCATTTCGCCGCTGGAGCAACTGGCGTTCCTGCGCAAGCTGGTCAACCGCCAATTGCCGCTCAAGCCCGCGGCCTACGATCTGGCCGAGACGCTGTTCGACGCCGGCGAGGCCGGCGGCTGGCGCCTGTATGGCAAGACCGGCACCGGCTCGCCGGGCAGCAACGGCGTCTACACGCCGGACAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAACTGGTGTTCGCGCGCCTGCTGCAGGACGAGAAAGCCACCCGGCCCAATGCCGGCCTGCGCGCCCGCGACGAGCTGTTGCGCGAGTGGCCGGCCATGGCCGACGCGCCCCGCCAGTAG", "fmax": "828", "accession": "JX306689.2", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter dolens", "NCBI_taxonomy_id": "1287738", "NCBI_taxonomy_cvterm_id": "42832"}, "protein_sequence": {"accession": "AFR53898.2", "sequence": "MPLRLPLRALGAALSLFALAGAPASAAVLCTVVADAADGRIVFQQGTQAACAERYTPASTFKLPIALMGADAGILQGAHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFQYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKPAAYDLAETLFDAGEAGGWRLYGKTGTGSPGSNGVYTPDNAYGWFVGWARKDGRQLVFARLLQDEKATRPNAGLRARDELLREWPAMADAPRQ"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-364", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37951", "model_name": "OXA-364", "model_type_id": "40292"}, "3480": {"model_id": "3480", "ARO_accession": "3001534", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-346 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5674": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATACTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF048919.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AHN07464.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSILFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-346", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37934", "model_name": "OXA-346", "model_type_id": "40292"}, "3483": {"model_id": "3483", "ARO_accession": "3001559", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-373 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5677": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAACTTTACAGTTGGCTCTCATCGCCCTCATTACAACCTTCGGTTCTGCATGTACCACAATAAGCCCCTCAGTAGAAACAGCTAAAAATCACCAGCAACAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACGCAGCTACGGCAATGACTTGAGCCGTGCTCAGACAGCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACTGAGGTGTTTAAATGGGATGGTCAAAAGCGTAGTTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCTGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTCTAGACCTGATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTGCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA", "fmax": "825", "accession": "HG931732.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter johnsonii", "NCBI_taxonomy_id": "40214", "NCBI_taxonomy_cvterm_id": "39092"}, "protein_sequence": {"accession": "CDM87362.1", "sequence": "MKTLQLALIALITTFGSACTTISPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLRSYGNDLSRAQTAYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-373", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37959", "model_name": "OXA-373", "model_type_id": "40292"}, "3482": {"model_id": "3482", "ARO_accession": "3001558", "model_param": {"blastp_bit_score": {"param_value": "480", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-372 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5676": {"dna_sequence": {"partial": "0", "sequence": "ATGATGCATATTTTTTTGGTCTTTCTGATTCTTTGCTCAAATTTTGCTCTCGCTGAGGACAAAGCTATTTCGGCTATTTTTTCCACAGAAGGTGTTGATGGGACCATCATTTTGAAGTCGTTGCGAGGAGATAAGACAATCACGCACAATGATGCACGCGCTTCTCGCCGATTCGCGTCAGCCTCGACTTTCAAGATATTCAACACGCTGATTGCAGTTCAAGAAAACGTGGTGAGTTTGTCGGGTACTGCATTCCGATGGGATGGAAAAACGCATGACATCCCCGACTGGAACCGTGACCAAACACTTGAAAGCGCATTCAAAGTTTCTTGTGTGTGGTGCTATCAGGAAATCGCCAAGCAAGTGGGGGAAGAAACCTATCGCCGCTACCTTACGCTTGCGAGGTATGGTGTTCTGACCAACGTAGCCGACACTACAACCTTTTGGCTTGATGGCAGCTTTACGGTCAGCGCCGTCGAGCAGATTGCTCTGTTGGAAAAGATCTATCTGCGAGAACTTCCGTTCCGTGATGAAGCCTACGACGCTTTAAAGCAGGTAATGCTGGCAGAGCAGACCGACAGCTACAAACTTTACGCAAAGACTGGCTGGGCAGCAAGGATGAACCCCCAAATTGGGTGGTACGTTGGATATGTTGAAACATCCGATGACGTATGGTTTTTTGCCATCAATTTGACCTTGAGGTCGGAACTTGACTTAGGTTTGCGCCAGAAAATAACAAAGGCTGCGCTTAGGGCTGAACGCATTATTCCCTGA", "fmax": "774", "accession": "KJ746496.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Citrobacter freundii", "NCBI_taxonomy_id": "546", "NCBI_taxonomy_cvterm_id": "36915"}, "protein_sequence": {"accession": "AIG22448.1", "sequence": "MMHIFLVFLILCSNFALAEDKAISAIFSTEGVDGTIILKSLRGDKTITHNDARASRRFASASTFKIFNTLIAVQENVVSLSGTAFRWDGKTHDIPDWNRDQTLESAFKVSCVWCYQEIAKQVGEETYRRYLTLARYGVLTNVADTTTFWLDGSFTVSAVEQIALLEKIYLRELPFRDEAYDALKQVMLAEQTDSYKLYAKTGWAARMNPQIGWYVGYVETSDDVWFFAINLTLRSELDLGLRQKITKAALRAERIIP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-372", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37958", "model_name": "OXA-372", "model_type_id": "40292"}, "3485": {"model_id": "3485", "ARO_accession": "3001578", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-392 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5680": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCAATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGCGCAGCGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAATCCCAAAAGGAATGGAAATTTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAAAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCGGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTTCCAGTTAGAAATTCAGCCATAGAAAACACCATAGATAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTTACAGCAAATAGAACCCTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCAATCACCATTCTAAACACACTAAATTTATAA", "fmax": "998", "accession": "AY139600.1", "fmin": "167", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "AAN41430.1", "sequence": "MKNTIHINFAIFLIIANIIYSSASASTDISTVASQLFEGTEGCFLLYDASTNAEIAQFNKAKCAAQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKIPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVRNSAIENTIDNMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-392", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37978", "model_name": "OXA-392", "model_type_id": "40292"}, "3484": {"model_id": "3484", "ARO_accession": "3004730", "model_param": {"blastp_bit_score": {"param_value": "1000", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "A pleuromutilin resistance gene encoding a predicted ABC-F transporter. The presence of inhibitory or sub-inhibitory concentrations of tiamulin showed that tva(A) confers reduced pleuromutilin susceptibility that does not lead to clinical resistance but facilitates the development of higher-level resistance via mutations in genes encoding ribosome-associated functions.", "model_sequences": {"sequence": {"5679": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTATAAAATTCAATAAAGTTTCTTTTTCTTATGATAGTTCTGATAATATATTAAATGATGTTTCTTTTCATATAGATAATTCATGCACTGCAATAGTAGGTGAAAATGGATGCGGTAAAACCACGCTAGCTAAACTTATAACAGGTATATTAAAGCCTAATTCAGGAAGCATAGAATATTCAAATAAAAATATTATAACTGCTTACTGCGATCAGGAATGTATCAACTTACCTGATAATGCTGAAAATTTATTTTATGATGATAGTTCATACTCAGGATATTTAACTTCTATATTTAAAATAGATTATAATTATTTATATAGATTTGATACTCTTAGTTTCGGAGAGAGAAAAAGACTACAAATAGCTTCTGCTTTATACTCTAATCCTGATATATTGGTATTAGATGAGCCTACGAATCATATTGATATAGAATGCAAAGATATACTTATTAATGTAATAAAAAGACTCGATTGTATAGTTATAATTATAAGCCATGATATTGATTTTCTTGATGAGTTAGTAGAAAAATGTATATTTATAAGAAATGGAAATTGCAAGATAAGAATAGGTAATTACACTCAATGCAGAGGATATGAAAAAGACGAAGAAGATTATAATTTTAGTTTATATGAGGAAAGCAGGAAGAAAGCTAAAATATTAGAAAATAGATACAAAAAACTACAAAATGAATCGGATGCTAAAAAAAGCAAATGCGGAAGTAAAAGACATATAGATAAAAAAGATCATGATGCTAAGGGAAAAATAGACGCAGCAAGACTTGCAGGTAAAGATTCAAGACTTGCAACTAAGGCTAAGCAGGCCAAAAGTTTATACAATAATACAGTAATGGAAATGGAATCTCTTTATACTAAGAAAAGAGAAGTTATGGATATGGAGTTTATTGGAGAAAGGTATAAAGGAAAATTTTTATTTTATCTTGAGGCAGGAGAAACAAAAATAAATAGTATAGTTCTAAGACATCCCGAACTTATAGTGAAAAAAGACAGCAGAATAGGTATTGAAGGTGTAAACGGGGCAGGTAAAACCAGTTTATTAAATTATATAATTGAAACAATGTATGATAATTCTATAGATAAAGAAAAGATAATATATATTCCTCAGGATATAGATAGAGAAAGTTGGAATAATACTTTTAATAATATAAAGGCATTGGATCATGAATCATTAGGTTTTTTAATGAGTTTTGTAAATAGACTAGGAAGCAATGCTAAATCTGTGATTAATTCATTGAATCATAGTCCGGGTGAGATGCGTAAAATAATGCTTGGAATGGCGGTTATAAAAAAGCCTTATATTATAATGTTAGATGAGCCTACGAATCATCTGGATATAGACTCAATAGAGCGTTTAGAGGAGGCTTTAATTTCTTTTAATTGTGCTTTGATTATAGTAAGTCATAATAGAAATTTTATTAAAAATGCAGTAAATACTTTATGGAGTATAAAAATAGAATATAATTACAGTATTTTAGATATTAAAAACACTATATAA", "fmax": "1518", "accession": "LT970863.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira hyodysenteriae", "NCBI_taxonomy_id": "159", "NCBI_taxonomy_cvterm_id": "42835"}, "protein_sequence": {"accession": "SOX29786.1", "sequence": "MFIKFNKVSFSYDSSDNILNDVSFHIDNSCTAIVGENGCGKTTLAKLITGILKPNSGSIEYSNKNIITAYCDQECINLPDNAENLFYDDSSYSGYLTSIFKIDYNYLYRFDTLSFGERKRLQIASALYSNPDILVLDEPTNHIDIECKDILINVIKRLDCIVIIISHDIDFLDELVEKCIFIRNGNCKIRIGNYTQCRGYEKDEEDYNFSLYEESRKKAKILENRYKKLQNESDAKKSKCGSKRHIDKKDHDAKGKIDAARLAGKDSRLATKAKQAKSLYNNTVMEMESLYTKKREVMDMEFIGERYKGKFLFYLEAGETKINSIVLRHPELIVKKDSRIGIEGVNGAGKTSLLNYIIETMYDNSIDKEKIIYIPQDIDRESWNNTFNNIKALDHESLGFLMSFVNRLGSNAKSVINSLNHSPGEMRKIMLGMAVIKKPYIIMLDEPTNHLDIDSIERLEEALISFNCALIIVSHNRNFIKNAVNTLWSIKIEYNYSILDIKNTI"}}}}, "ARO_category": {"37716": {"category_aro_name": "pleuromutilin", "category_aro_cvterm_id": "37716", "category_aro_accession": "3001317", "category_aro_class_name": "Antibiotic", "category_aro_description": "Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound."}, "37014": {"category_aro_name": "pleuromutilin antibiotic", "category_aro_cvterm_id": "37014", "category_aro_accession": "3000670", "category_aro_class_name": "Drug Class", "category_aro_description": "Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes."}, "35919": {"category_aro_name": "macrolide antibiotic", "category_aro_cvterm_id": "35919", "category_aro_accession": "0000000", "category_aro_class_name": "Drug Class", "category_aro_description": "Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins."}, "41687": {"category_aro_name": "ABC-F ATP-binding cassette ribosomal protection protein", "category_aro_cvterm_id": "41687", "category_aro_accession": "3004469", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A subfamily of the ATP-binding cassette protein superfamily. Unlike other ABC proteins, ABC-F genes are not fused to a transmembrane domain nor associated with transport. It has been shown that ABC-F proteins confer antibiotic resistance via ribosomal protection and not antibiotic efflux as in other ABC proteins."}, "35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}, "35945": {"category_aro_name": "streptogramin antibiotic", "category_aro_cvterm_id": "35945", "category_aro_accession": "0000026", "category_aro_class_name": "Drug Class", "category_aro_description": "Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30."}, "36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "36218": {"category_aro_name": "oxazolidinone antibiotic", "category_aro_cvterm_id": "36218", "category_aro_accession": "3000079", "category_aro_class_name": "Drug Class", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use."}, "36526": {"category_aro_name": "phenicol antibiotic", "category_aro_cvterm_id": "36526", "category_aro_accession": "3000387", "category_aro_class_name": "Drug Class", "category_aro_description": "Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome."}, "35936": {"category_aro_name": "lincosamide antibiotic", "category_aro_cvterm_id": "35936", "category_aro_accession": "0000017", "category_aro_class_name": "Drug Class", "category_aro_description": "Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides."}}, "ARO_name": "tva(A)", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42834", "model_name": "tva(A)", "model_type_id": "40292"}, "3487": {"model_id": "3487", "ARO_accession": "3001587", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-401 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5682": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCGCCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGCCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAAGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ780076.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AIS39034.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATATEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKRIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-401", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37987", "model_name": "OXA-401", "model_type_id": "40292"}, "3486": {"model_id": "3486", "ARO_accession": "3001586", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-400 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5681": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGATGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ780078.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AIS39036.1", "sequence": "MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLMGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-400", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37986", "model_name": "OXA-400", "model_type_id": "40292"}, "3405": {"model_id": "3405", "ARO_accession": "3001588", "model_param": {"blastp_bit_score": {"param_value": "555", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-402 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5600": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCGGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KJ780077.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AIS39035.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVRPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-402", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37988", "model_name": "OXA-402", "model_type_id": "40292"}, "3407": {"model_id": "3407", "ARO_accession": "3001707", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-103 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5602": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAGTAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA", "fmax": "292379", "accession": "APQF01000011.1", "fmin": "291557", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter radioresistens DSM 6976 = NBRC 102413 = CIP 103788", "NCBI_taxonomy_id": "981334", "NCBI_taxonomy_cvterm_id": "42784"}, "protein_sequence": {"accession": "ENV88740.1", "sequence": "MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-103", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38107", "model_name": "OXA-103", "model_type_id": "40292"}, "3406": {"model_id": "3406", "ARO_accession": "3001452", "model_param": {"blastp_bit_score": {"param_value": "420", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-140 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5601": {"dna_sequence": {"partial": "1", "sequence": "TTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATG", "fmax": "706", "accession": "KR780479.1", "fmin": "0", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae subsp. pneumoniae", "NCBI_taxonomy_id": "72407", "NCBI_taxonomy_cvterm_id": "39097"}, "protein_sequence": {"accession": "ALL27283.1", "sequence": "FAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKY"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-140", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37852", "model_name": "OXA-140", "model_type_id": "40292"}, "3409": {"model_id": "3409", "ARO_accession": "3001445", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-123 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5604": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "EU255292.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ABX45062.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-123", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37845", "model_name": "OXA-123", "model_type_id": "40292"}, "3408": {"model_id": "3408", "ARO_accession": "3001444", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-122 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5603": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTGCTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "EU255291.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ABX45061.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEIAYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-122", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37844", "model_name": "OXA-122", "model_type_id": "40292"}, "3562": {"model_id": "3562", "ARO_accession": "3004755", "model_param": {"blastp_bit_score": {"param_value": "780", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BIL-1 is a plasmid-borne beta-lactamase that is also a class C beta-lactamase.", "model_sequences": {"sequence": {"5757": {"dna_sequence": {"partial": "0", "sequence": "ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCCGCGATGCTATCGCGCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGCGTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACACGAAAGTGGCATTGGCAGCCGTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATCGTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA", "fmax": "1272", "accession": "X74512.1", "fmin": "126", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "CAA52618.1", "sequence": "MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGRDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWAYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDTKVALAAVPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVIVANKSYPNPVRVEAAWRILEKLQ"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42866": {"category_aro_name": "BIL Beta-lactamase", "category_aro_cvterm_id": "42866", "category_aro_accession": "3004754", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BIL beta-lactamase is plasmid-borne and is a class C beta-lactamase."}}, "ARO_name": "BIL-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42867", "model_name": "BIL-1", "model_type_id": "40292"}, "3563": {"model_id": "3563", "ARO_accession": "3004757", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BKC-1 is a beta-lactamase conferring resistance to carbapenem and is found in Brazilian Klebsiella.", "model_sequences": {"sequence": {"5758": {"dna_sequence": {"partial": "0", "sequence": "ATGACGATCACATTTTCGCGCCGGCAGGCGATTGCCGGCGCTCTCCTTGCCGTTCCCGCCGTGTCCACGCTGGCCGCCAGCGCCGGCGCTCTCCTTGCCGTTCCCGCCGTGTCCACGCTGGCCGCCAGCGCCGGGGCGGCCACGGGCGGCCCGCTGGAAAAGAGGCTGGCCGAGCTGGAAGGGCGTCACAAGGGCCGCATCGGCGTTGCCATACATAATCTCGCAACGGGCGCCCGCATCGGCCACCGGGCGGACGAGCGCTTCCTGATGTGCAGCACCTTCAAGGCGTTGCTGGCGGCCCATATCCTCGCCCGCGTCGACAGGAAGGAAGAAACGCTCGACCGGCGGATCGTCGTCGGGAAATCCGATCTTGTGGACTGGTCGCCGGTGGTGGAAACCCGTGTCGGCGGCGAGGGCATCTCGATTGCCGAGCTTTGCGAGGCGGCGATCACGCTCAGCGACAACGCCGCGGCCAATCTCCTGCTGTCCGCCTCGGGCGGGCCGAAGGCCGTCACGCAGTTCCTGCGCGGTTTCGGCGACGACGTGACGCGCCTCGACCGCACCGAACCGACGCTCAACTATCGCGAGACGCCGGACGACGAGCGCGACACGACCACGCCCGCCGCCATGGCCGAGACGCTGCGCAAGCTGATCATCGGCGATGTCCTCGCGCGCGGCTCGAAGGCGCAGCTTGCCGCCTGGCTGGTGATGAACAAGACCGGCGACACGCGATTGCGCGCCGGCTTCCCGGTCGACTGGACGACCGGCGACAAGACCGGCACGAACGGCGACAGGCACGGCAACGCCAACGATGTCGCCATCGCCTGGTCGCCGGATCGCGGCGCGGTGGTCGTCACCGCTTTCTGCGAGATTCCCGGCATTTCCGGGGATGAGCGCAACGCCGTCATCGCCGAGATTGGTCGCATTGCCGCCGAGGCCTGA", "fmax": "9544", "accession": "KP689347.1", "fmin": "8602", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "AKD43328.1", "sequence": "MTITFSRRQAIAGALLAVPAVSTLAASAGALLAVPAVSTLAASAGAATGGPLEKRLAELEGRHKGRIGVAIHNLATGARIGHRADERFLMCSTFKALLAAHILARVDRKEETLDRRIVVGKSDLVDWSPVVETRVGGEGISIAELCEAAITLSDNAAANLLLSASGGPKAVTQFLRGFGDDVTRLDRTEPTLNYRETPDDERDTTTPAAMAETLRKLIIGDVLARGSKAQLAAWLVMNKTGDTRLRAGFPVDWTTGDKTGTNGDRHGNANDVAIAWSPDRGAVVVTAFCEIPGISGDERNAVIAEIGRIAAEA"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42868": {"category_aro_name": "BKC Beta-lactamase", "category_aro_cvterm_id": "42868", "category_aro_accession": "3004756", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BKC beta-lactamase is a class A beta-lactamase."}}, "ARO_name": "BKC-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42869", "model_name": "BKC-1", "model_type_id": "40292"}, "3560": {"model_id": "3560", "ARO_accession": "3004751", "model_param": {"blastp_bit_score": {"param_value": "590", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BES-1 is a class A beta-lactamase that is found in Serratia marcescens.", "model_sequences": {"sequence": {"5755": {"dna_sequence": {"partial": "0", "sequence": "ATGTGGCAGTGGCTTGGAAAAGTGCGGTGGTTGCTGGTGGTGATAGCGCTGCTGGGTGGCAAGGTCATGGCGGCGTCTGAACTGGATAGCGCGCTGGCCAGACTCGAGCAGCAGCATCATGGGCGTCTGGGGCTGGCCTATATCGATAGTGGCAGCGGCGAGAGTTACAGCTATCGCGGTGAGGAGCGTTTTGCCTTTTGCAGCACCTTCAAGGCGGTGCTGGCGGGGGCGGTGCTGCAGCGAAGCGTCAGTCAGCCCGGTTTGCTCGATAAGCGGGTGCATTATGCGGCCACGGATCTGCTCGCCTATGCCCCCATCACCAAGACGCATCTGGATAAAGGGATGCGCATCGGTGAACTGGCCGCAGCGGCGGTGCAATATAGTGACAACACGGCGGCCAACCTGCTGCTGCAAGAAATTGGCGGCGTCCAGGCGCTGAACCGGTTTGTGCAGGGGTTGGGAGATCCGGCATTCCGTCTGGATAGGATAGAGCCTCACCTTAATAGTGCCGAGCCAGGAGATGTGCGCGATACCACCACGCCGCTGGCCATGGCCCACACCCTGCAGGCCATGACTCTGGGCAAGGGGTTACCACAGGCCCAGCAGGCGCAACTGGTGAGCTGGCTTAAAGGCAATACCACGGGGGCACAGCGTATTCAAGCTGGCGTACCGGCAGGCTGGCAGGTAGGCGACAAGACTGGCACAGGTGGTTACGGCACCACCAACGATATCGCCATCCTCTGGCCGGAGCAGGGTGCTCCCAAGGTGCTGGCCATCTACTTTACCCAGCCCGCAGCCGATGCCGAGGCCAACCGCGCCATACTGGCCGAAGCCACCCGACTGGTACTGCAAGATAAAAGTATCAATAAAATCAAGTAG", "fmax": "1068", "accession": "AF234999.1", "fmin": "189", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia marcescens", "NCBI_taxonomy_id": "615", "NCBI_taxonomy_cvterm_id": "36783"}, "protein_sequence": {"accession": "AAF61147.1", "sequence": "MWQWLGKVRWLLVVIALLGGKVMAASELDSALARLEQQHHGRLGLAYIDSGSGESYSYRGEERFAFCSTFKAVLAGAVLQRSVSQPGLLDKRVHYAATDLLAYAPITKTHLDKGMRIGELAAAAVQYSDNTAANLLLQEIGGVQALNRFVQGLGDPAFRLDRIEPHLNSAEPGDVRDTTTPLAMAHTLQAMTLGKGLPQAQQAQLVSWLKGNTTGAQRIQAGVPAGWQVGDKTGTGGYGTTNDIAILWPEQGAPKVLAIYFTQPAADAEANRAILAEATRLVLQDKSINKIK"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42862": {"category_aro_name": "BES Beta-lactamase", "category_aro_cvterm_id": "42862", "category_aro_accession": "3004750", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BES beta-lactamase is a class A beta-lactamase family."}}, "ARO_name": "BES-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42863", "model_name": "BES-1", "model_type_id": "40292"}, "3561": {"model_id": "3561", "ARO_accession": "3004753", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BIC-1 is a beta-lactamase conferring resistance to carbapenems that is found in Pseudomonas fluorescens.", "model_sequences": {"sequence": {"5756": {"dna_sequence": {"partial": "0", "sequence": "ATGGCACGTCCTTCTAAACTAGCTTTATCATTTTCTCTTCTGTTGCCTTTTTTACCCTTCACCAGCTTCGCTGAAACCTGGCCACAGGGCGATATCGCCCGACAAAAAATCGTAAAGCTGGAAAAGGATTTTGGTGGGCGGATTGGAGTATCTGCCATCGATACGGGCGCCAATCGAACTTTTGACTTTCGAGCGGACGAACGTTTCCCTTTATGCAGCTCCTTTAAGGGCTTTCTGGCTGGCGCCGTGCTCTCCCACAGCCAACAGCAGGAAGGCTTACTGGAGAAACGTATCGACTATAAGAATCGGGTGATGGAACCTCACTCTCCCATCAGCGCACAACATAGTTCGACGGGTATGACCGTGGCGCAATTAGCGGCAGCGGCGCTGCAGTACAGCGACAACGGTGCGACAAATTTGCTTCTGGAAAACGTTCTGGGCGGGCCCGCCGGGATGACGACCTTCATGAGGACCTTAGGCGATACAACGTTTCGCTTAGATCGATGGGAACTCGAACTCAATAGCGCCATTCCGGGCGACGATCGAGATACCTCGACCCCCCACGCCATAGCCCGCAGCTTGCAAAAAATAGCGTTGGGTGAGGCGTTGCAAACCGCACCGCGTCAGCAGCTGGTTGATTGGCTCATCGGAAATACGACAGGTGGAGCGCGGATCCGGGCAGGCGTTCCTGTCGAGTGGGTTGTAGGGGATAAAACGGGCACGTGCGGTGTGTACGGCACCGCCAATGATTATGCCGTCATATGGCCAAAAACATCCGCCCCGATTGTCTTGGCGATTTACACCGCGAAACCGAACAAGGAGGACAAACATAGCGATGCCGTTATTGCCGAAGTGACCCGTGCCGTTCTGGAAAGCTTTGAATAA", "fmax": "885", "accession": "GQ260093.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas fluorescens", "NCBI_taxonomy_id": "294", "NCBI_taxonomy_cvterm_id": "36937"}, "protein_sequence": {"accession": "ADB56658.1", "sequence": "MARPSKLALSFSLLLPFLPFTSFAETWPQGDIARQKIVKLEKDFGGRIGVSAIDTGANRTFDFRADERFPLCSSFKGFLAGAVLSHSQQQEGLLEKRIDYKNRVMEPHSPISAQHSSTGMTVAQLAAAALQYSDNGATNLLLENVLGGPAGMTTFMRTLGDTTFRLDRWELELNSAIPGDDRDTSTPHAIARSLQKIALGEALQTAPRQQLVDWLIGNTTGGARIRAGVPVEWVVGDKTGTCGVYGTANDYAVIWPKTSAPIVLAIYTAKPNKEDKHSDAVIAEVTRAVLESFE"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42864": {"category_aro_name": "BIC Beta-lactamase", "category_aro_cvterm_id": "42864", "category_aro_accession": "3004752", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BIC is a class A beta-lactamase conferring resistance to carbapenem."}}, "ARO_name": "BIC-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42865", "model_name": "BIC-1", "model_type_id": "40292"}, "3566": {"model_id": "3566", "ARO_accession": "3004762", "model_param": {"blastp_bit_score": {"param_value": "634", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BRO-2 is a class A beta-lactamase found in M.catarrhalis.", "model_sequences": {"sequence": {"5761": {"dna_sequence": {"partial": "0", "sequence": "ATGATGCAACGCCGTCATTTTTTACAAAAAACCTTATTGGCACTACCTATTATTTTTTCTGGCAATTTATTAACTGGATGTAAAACGAATTTGTCTGATGATTATTTGCCCGATGACAAGATAACAAACAATCCAAATTTATTACAAAATAAATTAAAAGAGATATTGCCAATTTGGGAAAATAAATTTAATGCCAAAATTGGTATGACGATTATTGCTGACAATGGTGAACTATCCAGTCATCGTGGTAATGAATATTTTCCTGTTAATAGTACCATTAAAGCCTTTATTGCAAGTCATATATTATTACTTGTAGATAAAGAAAAATTGGATTTAAACGAAAAAATCATCATTAAAGAAAGCGATTTGATAGAATATTCTCCTGTCTGTAAAAAATACTTTGATGAGAATAAACCAATTTCTATTAGTGAATTGTGCGAAGCTACCATAACACTGAGTGATAATGGTTCTGCTAATATCTTGTTGGATAAAATTGGGGGTTTGACTGCATTCAATCAATTTTTGAAAGAGATTGGGGCGGATATGGTGCTGGCAAATAATGAACCTTTATTAAATCGCTCACATTATGGTGAAACCAGTGATACCGCAAAACCAATTCCTTACACAAAAAGCCTAAAAGCACTGATTGTAGGCAATATCCTATCCAATCAAAGCAAAGAACAGTTGATAACTTGGCTTATCAACGATAAAGTTGCTGATAATTTATTGAGAAAATATTTACCAAAAAATTGGCGAATTGGCGACAAAACAGGCACAGGTAGTGAATCAAAAAATATCATTGCTGTGATTTGGAATGAAAATAATAAACCTTATTTTATCAGCCTATTTATCACCCAGCCCCATGATGGTAAATCCCTTGGTTTTAAAAATCAAAAAGATGAAATAATGGCACAAATTGGTAAAGAAATTTATCCATTTTTATAA", "fmax": "1007", "accession": "Z54181.1", "fmin": "62", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella catarrhalis ATCC 43617", "NCBI_taxonomy_id": "857580", "NCBI_taxonomy_cvterm_id": "42876"}, "protein_sequence": {"accession": "CAA90891.1", "sequence": "MMQRRHFLQKTLLALPIIFSGNLLTGCKTNLSDDYLPDDKITNNPNLLQNKLKEILPIWENKFNAKIGMTIIADNGELSSHRGNEYFPVNSTIKAFIASHILLLVDKEKLDLNEKIIIKESDLIEYSPVCKKYFDENKPISISELCEATITLSDNGSANILLDKIGGLTAFNQFLKEIGADMVLANNEPLLNRSHYGETSDTAKPIPYTKSLKALIVGNILSNQSKEQLITWLINDKVADNLLRKYLPKNWRIGDKTGTGSESKNIIAVIWNENNKPYFISLFITQPHDGKSLGFKNQKDEIMAQIGKEIYPFL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42873": {"category_aro_name": "BRO Beta-lactamase", "category_aro_cvterm_id": "42873", "category_aro_accession": "3004760", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BRO is a class A beta-lactamase that is found in M.catarrhalis."}}, "ARO_name": "BRO-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42875", "model_name": "BRO-2", "model_type_id": "40292"}, "3567": {"model_id": "3567", "ARO_accession": "3004764", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CBP-1 is a class A beta-lactamase gene found in C. botulinum.", "model_sequences": {"sequence": {"5764": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAGTAAACTCAAAATTAAAGGTAAATAAATTTAAAATGTGTATATTTATATCAATTCTTATATTTTCTCTTACTGGATGTGGAAATGTAGAAAATAAAACTTCTGAAAATACAAAACCTGAGATACAATATAATTCAGCATTTTCAAAAATTGAAAGTGATTATGGTGTTAAACTTGGTGTATATGCTTTTGATACAGAAACAAATAAAGAAGTTACATATAATGCTGATAAGAGATTCGCTTACTGTTCTACCTTTAAATCTTTAATATCCGGTGCGATTTTACAAAAATATTCATCAGACCAACTTAAACAAGTAATTAAATATAGCCCAAAAGATGTACTGTCTTATGCACCAGTTACAAAAAATCATGTTGATAAAGGTATGACTATTGAAGAACTTTGCGATGCGGCAGTACGCTTTAGTGATAATACAGCTGCAAATCTTTTGATTAATCTTATAGGTGGACCTAATGGTTTTAAATCAGCACTTAATCAATTAGGTGACACAGTTACAGAACCTGCACGTATCGAACCAGAACTAAATGTTGCTACACCTGGAGATAATAGGGATACTAGTACTCCAAGACAATTATCAATTGATTTAAAAGAATACACAACTGGAAATATATTATCAGATGATAAGAAAAAAATTCTTATTAATTGGATGTCAGGAAATGCAACAGGTGATAAGCTAATTCGTGCAGGAGCACCAAAAGACTGGATGGTTTCTGATAAAAGTGGAACTGGTTCTTACGGAACAAGAAATGATATTGCAATAGTAATACCACCAAATAAAAAGCCTATATTTATTGCAATATTATCAAGTAAAAACGATAAAGATGCTAAATATGATGACAAAACAATTTCTGAGGCTTCTAAAATTGTATTTGATTATTTTATTAACACCAGGAAATAG", "fmax": "927", "accession": "KP718480.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridium botulinum", "NCBI_taxonomy_id": "1491", "NCBI_taxonomy_cvterm_id": "41649"}, "protein_sequence": {"accession": "ALF06101.1", "sequence": "MKKIVNSKLKVNKFKMCIFISILIFSLTGCGNVENKTSENTKPEIQYNSAFSKIESDYGVKLGVYAFDTETNKEVTYNADKRFAYCSTFKSLISGAILQKYSSDQLKQVIKYSPKDVLSYAPVTKNHVDKGMTIEELCDAAVRFSDNTAANLLINLIGGPNGFKSALNQLGDTVTEPARIEPELNVATPGDNRDTSTPRQLSIDLKEYTTGNILSDDKKKILINWMSGNATGDKLIRAGAPKDWMVSDKSGTGSYGTRNDIAIVIPPNKKPIFIAILSSKNDKDAKYDDKTISEASKIVFDYFINTRK"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42877": {"category_aro_name": "CBP beta-lactamase", "category_aro_cvterm_id": "42877", "category_aro_accession": "3004763", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CBP is a class A beta-lactamase family found in C. botulinum."}}, "ARO_name": "CBP-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42878", "model_name": "CBP-1", "model_type_id": "40292"}, "3564": {"model_id": "3564", "ARO_accession": "3004759", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BPU-1 is a class D beta-lactamase found in Bacillus pumilus.", "model_sequences": {"sequence": {"5759": {"dna_sequence": {"partial": "0", "sequence": "TTGAAGAAAAAGTATATAAAAAGGCTGTTTTCTTGCATCATGCTGATGGCATTTTGTATCAGCCAGCCATCATCAACTGAAGCAAGATCAATAGCGTGGTCTGTAGATGAATTCTTTAAAAATCGGGAAGGCACGTTTGTGATTCAAGAAGTAAAAGAAAAGTCCCCATGGGTGTATAACAAAAAAAGAGCGAAAGAGCGCTTTGCACCTCAATCGACATTTAAGGTAGCAAATGCCTTAATCGGACTCCAAACAGGCGCAGTGAGAGATGAATACGACATCAAATATTGGGATGGCGTAAAAAGAGAGATTGACAATTGGAATAGAGATCATACATTAGGATCTGGCATGAGAGATTCAGTCGTCTGGTACTATCAAGCCATGGCACGTGACATTGGAGAAGAACGCATGAATCATTGGGTGAAAGCTATTCATTATGGGAACAAAGACATATCTGGCGGAATCGATCAATTTTGGTTAAGCAGTACCCTACGAATTTCTCCCATCGAACAAGTTCGTTTTCTCAAACAGCTATATGAAGAGACTCTTCCATTTGACCTAAAGAACATGAGAACAGTCAAACGAATGATGGTACAAGAAGAAGAGAAACACGCCACCCTATACGGAAAAACAGGCTCCGGATCAGACATCGGCTGGTACGTAGGTTTTATCAAACATGAACACAAAACCTACATCCTCGCCACAAATATCAAAGGCACCGGCATAGAAGCAAAAGACATCACCTATCGCATTTTGAAAAAATATCATTTGATGGAAGCATCCGTTTAG", "fmax": "2350187", "accession": "CP000813.4", "fmin": "2349398", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Bacillus pumilus SAFR-032", "NCBI_taxonomy_id": "315750", "NCBI_taxonomy_cvterm_id": "42872"}, "protein_sequence": {"accession": "ABV63006.2", "sequence": "MKKKYIKRLFSCIMLMAFCISQPSSTEARSIAWSVDEFFKNREGTFVIQEVKEKSPWVYNKKRAKERFAPQSTFKVANALIGLQTGAVRDEYDIKYWDGVKREIDNWNRDHTLGSGMRDSVVWYYQAMARDIGEERMNHWVKAIHYGNKDISGGIDQFWLSSTLRISPIEQVRFLKQLYEETLPFDLKNMRTVKRMMVQEEEKHATLYGKTGSGSDIGWYVGFIKHEHKTYILATNIKGTGIEAKDITYRILKKYHLMEASV"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42870": {"category_aro_name": "BPU Beta-lactamase", "category_aro_cvterm_id": "42870", "category_aro_accession": "3004758", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BPU is a class D beta lactamase gene family."}}, "ARO_name": "BPU-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42871", "model_name": "BPU-1", "model_type_id": "40292"}, "3565": {"model_id": "3565", "ARO_accession": "3004761", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "BRO-1 is a class A beta-lactamase found in M.catarrhalis.", "model_sequences": {"sequence": {"5760": {"dna_sequence": {"partial": "0", "sequence": "ATGATGCAACGCCGTCATTTTTTACAAAAAACCTTATTGGCACTACCTATTATTTTTTCTGGCAATTTATTAACTGGATGTAAAACGAATTTATCTGATGATTATTTGCCCGATGATAAGATAACAAACAATCCAAATTTATTACAAAATAAATTAAAAGAGATATTGCCAATTTGGGAAAATAAATTTAATGCCAAAATTGGTATGACGATTATTGCTGACAATGGTGAACTATCCAGTCATCGTGGTAATGAATATTTTCCTGTTAATAGTACCATTAAAGCCTTTATTGCAAGTCATATATTATTACTTGTAGATAAAGAAAAATTGGATTTAAACGAAAAAATCATCATTAAAGAAAGCGATTTGATAGAATATTCTCCTGTCTGTAAAAAATACTTTGATGAGAATAAACCAATTTCTATTAGTGAATTGTGCGAAGCTACCATAACACTGAGTGATAATGGTTCTGCTAATATCTTGTTGGATAAAATTGGGGGTTTGACTGCATTCAATCAATTTTTGAAAGAGATTGGGGCGGATATGGTGCTGGCAAATAATGAGCCTTTATTAAATCGCTCACATTATGGTGAAACCAGTGATACCGCAAAACCAATTCCTTACACAAAAAGCCTAAAAGCACTGATTGTAGGCAATATCCTATCCAATCAAAGCAAAGAACAGTTGATAACTTGGCTTATCAATGATAAAGTTGCTGATAATTTATTGAGAAAATATTTACCAAAAAATTGGCGAATTGGCGACAAAACAGGCACAGGTAGTGAATCAAAAAATATCATTGCTGTGATTTGGAATGAAAATAATAAACCTTATTTTATCAGCCTATTTATCACCCAGCCCCATGATGGTAAATCCCTTGATTTTAAAAATCAAAAAGATGAAATAATGGCACAAATTGGTAAAGAAATTTATCCATTTTTATAA", "fmax": "1028", "accession": "Z54180.1", "fmin": "83", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella catarrhalis", "NCBI_taxonomy_id": "480", "NCBI_taxonomy_cvterm_id": "41250"}, "protein_sequence": {"accession": "CAA90890.1", "sequence": "MMQRRHFLQKTLLALPIIFSGNLLTGCKTNLSDDYLPDDKITNNPNLLQNKLKEILPIWENKFNAKIGMTIIADNGELSSHRGNEYFPVNSTIKAFIASHILLLVDKEKLDLNEKIIIKESDLIEYSPVCKKYFDENKPISISELCEATITLSDNGSANILLDKIGGLTAFNQFLKEIGADMVLANNEPLLNRSHYGETSDTAKPIPYTKSLKALIVGNILSNQSKEQLITWLINDKVADNLLRKYLPKNWRIGDKTGTGSESKNIIAVIWNENNKPYFISLFITQPHDGKSLDFKNQKDEIMAQIGKEIYPFL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42873": {"category_aro_name": "BRO Beta-lactamase", "category_aro_cvterm_id": "42873", "category_aro_accession": "3004760", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "BRO is a class A beta-lactamase that is found in M.catarrhalis."}}, "ARO_name": "BRO-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42874", "model_name": "BRO-1", "model_type_id": "40292"}, "3568": {"model_id": "3568", "ARO_accession": "3004766", "model_param": {"blastp_bit_score": {"param_value": "590", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CGA-1 is a class A beta-lactamase gene found in Chryseobacterium gleum.", "model_sequences": {"sequence": {"5765": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAACAACACTTCTTTTTCTTCTGATTTCAGCATTTTCATTGGCTCAGACTTCTTTATTGGAACAAAAAATTAATTCAATCATTAAGAACAAAAAAGCTACAGTCGGTGTTTCTGTTCTTGGGTTTGAAAATGGCTTTAAGTACGATAAAAACGGAGATAAAAAACTCCCGATGCAAAGTGTGTTTAAATTTCACATTGCAGCAGCAGTCCTGAATGCTGTAGATCAGGGAAAACTTTCTCTGGATCAGAAAATTATGCTAAACCAATCGAATTTACTGGAAAATACATGGTCGCCGCTTCGTGATAAGTATCCGGCAGGAAATATTGAAATTCCGTTAAGCGAAGTGATTGAATATACAGTTGCCAAAAGTGACAATAATGGCTGTGATATTCTTCTGAGGCTGCTGGGAGGAACCCAGGTTGTCCAGAAGTTTATGGATTCTAAAGGAGTAAAAGGTTTTCAGATCAAATACAATGAAGAGGATATGCATAAAGACTGGAATGTTCAGTATGAAAATTATAGTACTACAAAATCCGCTGCTGATGTCCTGAAAAAGTTGTATGACGGAAAATTATTATCCAAAAAATCCACAGACTATCTGATGAAAGTAATGCTTTCTACTTCAACCGGATTGAATAAAATGGTGGAACAGCTTCCCAAAAACACACCTGTCGCAAGAAAAACGGGAGCTTCCGGGAAGAATAATGCCGGTTTAACAGGCGCAGAAAATGAAATCGGAATTGTTACTTTACCCAACGGGAAACATTATGCATTAGCTGTATTTGTCAGTAATTCAATGGAAACGGATGCAGTGAACTGCAGGATGATTTCAGATATTTCGAAGGAGGTTTGGGAATATTTTAATAAATAA", "fmax": "1315", "accession": "AF339733.1", "fmin": "436", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Chryseobacterium gleum", "NCBI_taxonomy_id": "250", "NCBI_taxonomy_cvterm_id": "39078"}, "protein_sequence": {"accession": "AAL55262.1", "sequence": "MKKTTLLFLLISAFSLAQTSLLEQKINSIIKNKKATVGVSVLGFENGFKYDKNGDKKLPMQSVFKFHIAAAVLNAVDQGKLSLDQKIMLNQSNLLENTWSPLRDKYPAGNIEIPLSEVIEYTVAKSDNNGCDILLRLLGGTQVVQKFMDSKGVKGFQIKYNEEDMHKDWNVQYENYSTTKSAADVLKKLYDGKLLSKKSTDYLMKVMLSTSTGLNKMVEQLPKNTPVARKTGASGKNNAGLTGAENEIGIVTLPNGKHYALAVFVSNSMETDAVNCRMISDISKEVWEYFNK"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42879": {"category_aro_name": "CGA beta-lactamase", "category_aro_cvterm_id": "42879", "category_aro_accession": "3004765", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CGA is a class A beta-lactamase family that is found in Chryseobacterium gleum."}}, "ARO_name": "CGA-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42880", "model_name": "CGA-1", "model_type_id": "40292"}, "3478": {"model_id": "3478", "ARO_accession": "3001532", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-344 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5672": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF048917.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AHN07462.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-344", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37932", "model_name": "OXA-344", "model_type_id": "40292"}, "3474": {"model_id": "3474", "ARO_accession": "3001528", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-340 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5668": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "66595", "accession": "NGCN01000023.1", "fmin": "65770", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "OTK94966.1", "sequence": "MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-340", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37928", "model_name": "OXA-340", "model_type_id": "40292"}, "3475": {"model_id": "3475", "ARO_accession": "3001529", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-341 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5669": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACCCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATATATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF048913.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AHN07458.1", "sequence": "MNIKAPLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNIFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYRSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-341", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37929", "model_name": "OXA-341", "model_type_id": "40292"}, "3476": {"model_id": "3476", "ARO_accession": "3001530", "model_param": {"blastp_bit_score": {"param_value": "535", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-342 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5670": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCGAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF048915.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AHN07460.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFREWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-342", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37930", "model_name": "OXA-342", "model_type_id": "40292"}, "3477": {"model_id": "3477", "ARO_accession": "3001531", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-343 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5671": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGATTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "12964", "accession": "NWUK01000007.1", "fmin": "12139", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "PCE45447.1", "sequence": "MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWIVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-343", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37931", "model_name": "OXA-343", "model_type_id": "40292"}, "3470": {"model_id": "3470", "ARO_accession": "3001763", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-308 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5664": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAAAAATTGAATTTGGCACTTTTGTGTTTTTTGAGTATTTTGTGTGCAGCTTGTCAGTCTAATCAACAACTGTCGGCTAATTCACATACTGAAAACCACAATACCCGTGCAGCAGAAATCTCGCTTCTTTTCGATGAGATGCATACTCAAGCAGTATTTGTGACCTATGACGGTCAGCATTTTCAGAGCTACGGTAATGCTTTACAAAGAGCAGATACTGCCTACGTTCCTGCTTCGACATTTAAAATGTTAAATGCATTGATTGGACTGCAAAATCATAAAGCAACCAACACCGAAGTCTTTAAATGGGATGGTCAAAAAAGGGCAATGTCGATCTGGGAAAAAGACATGACCTTATCCGATGCCATGAAAGTTTCAGCTGTACCGGTTTATCAAGAATTGGCGCGTCGTATTGGCTTGGATTTGATGCAAAAGGAAGTAACGCGGGTTAGATATGGCAATACGGATATCGGCACTGTTGTTGATCGTTTTTGGCTAGATGGACCACTGAAGATCACACCTAAACAAGAAGCCCAATTTGCATATCAATTGGCAACACAACAATTGCCATTTGATCAAAATGTGCAAAGCCAAGTTAAAGATATGTTGTATGTGGAAAGTCGAGGGCAATCCAAGCTTTTTGCCAAGTCTGGTTTGAGCATGAAAAATGGGCAACCTGACATCGGTTGGTATACGGGTTGGGTTGAACAAGCCGATGGCAAAATTGTGGCTTTTTCCATCAATATGCAAATGGTACAGGGGCTAGATGTCAATAGCCGTCAGCAGGCAACACTGGATATCTTAGATAAATTGGGCATATTTTTTTATTTATAA", "fmax": "349338", "accession": "APPN01000080.1", "fmin": "348498", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter gerneri DSM 14967 = CIP 107464", "NCBI_taxonomy_id": "1120926", "NCBI_taxonomy_cvterm_id": "41193"}, "protein_sequence": {"accession": "ENV32314.1", "sequence": "MNKKLNLALLCFLSILCAACQSNQQLSANSHTENHNTRAAEISLLFDEMHTQAVFVTYDGQHFQSYGNALQRADTAYVPASTFKMLNALIGLQNHKATNTEVFKWDGQKRAMSIWEKDMTLSDAMKVSAVPVYQELARRIGLDLMQKEVTRVRYGNTDIGTVVDRFWLDGPLKITPKQEAQFAYQLATQQLPFDQNVQSQVKDMLYVESRGQSKLFAKSGLSMKNGQPDIGWYTGWVEQADGKIVAFSINMQMVQGLDVNSRQQATLDILDKLGIFFYL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-308", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38163", "model_name": "OXA-308", "model_type_id": "40292"}, "3471": {"model_id": "3471", "ARO_accession": "3001524", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-336 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5665": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAAATACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF048907.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AHN07452.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKNTPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-336", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37924", "model_name": "OXA-336", "model_type_id": "40292"}, "3472": {"model_id": "3472", "ARO_accession": "3001525", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-337 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5666": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTACAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "161003", "accession": "PYSX01000023.1", "fmin": "160178", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "RIL13772.1", "sequence": "MNITALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-337", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37925", "model_name": "OXA-337", "model_type_id": "40292"}, "3473": {"model_id": "3473", "ARO_accession": "3001527", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-339 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5667": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTAATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTTATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF048911.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AHN07456.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-339", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37927", "model_name": "OXA-339", "model_type_id": "40292"}, "3575": {"model_id": "3575", "ARO_accession": "3004775", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CME-1 is a class A beta-lactamase gene belonging to Chryseobacterium meningosepticum.", "model_sequences": {"sequence": {"5771": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATTATACTCCTATTTATCTTGACAAGCCAGTTGGTGCTTGCTCAACATACTTCAATATTAAATGATATAAATGCTGTTACCAAAGACAAGAAAGCCACAGTAGCTGTTTCTGTTTTGGGGATAGAAAATGATTTTCAGTTTAGTAACGCCAATGGTAATTTGAAAATGCCGATGCTGAGTGTTTTTAAATTTCATATTGCATTGGCGGTTCTAAATCAGGTAGACAAAGGTAACCTTACCTTGGATCAGAAAATACTGATTAAAAAATCGGATCTATTAGAAAATACATGGTCACCACTTCGTGAGAAGTATCCGGATGGAAATGTAGAACTTCCTTTAAGCGAAATTATTACTTATACCGTAGCCCAAAGTGACAACAACGGATGCGACATACTATTAAGGCTAATTGGCGGGACTAAAACTGTTCAGAAATTAATGGATGTGAATGGTATAAAAAACTTTCAGATAAAATATAATGAGGAAGAAATGCATAAAAATGATGTAAAAACTCTTTATGCAAATTACACGACCACAGCATCTATGGTAAAAACTCTGAAAGCGTTCTATAAAGGAATGTTTTTATCAAAAAGATCCACAATTTTTCTAATGGATATTATGACTAAAACCAATACCGGAATGTCAAAGCTTCCGGGCTTGCTGCCAAAAGTTAGAATGGCCAGAAAAACAGGTTCTTCGGGTAAAATGAAAAACGGATTAACGATTGCTGAGAACGATTCAGGAATTGTAACTTTAGCAAATGGTAAACATTATGCAATTGCAGTATTTGTAAAGGACTCTATGGAAAGTGAGGAAGTCAATTGTGGAATGATTGCCCAGGTCTCGAAAATTGTCTGGGATGCTTTAAATAAAAAAAAATAA", "fmax": "959", "accession": "AJ006275.1", "fmin": "71", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "CAB55427.1", "sequence": "MKKIILLFILTSQLVLAQHTSILNDINAVTKDKKATVAVSVLGIENDFQFSNANGNLKMPMLSVFKFHIALAVLNQVDKGNLTLDQKILIKKSDLLENTWSPLREKYPDGNVELPLSEIITYTVAQSDNNGCDILLRLIGGTKTVQKLMDVNGIKNFQIKYNEEEMHKNDVKTLYANYTTTASMVKTLKAFYKGMFLSKRSTIFLMDIMTKTNTGMSKLPGLLPKVRMARKTGSSGKMKNGLTIAENDSGIVTLANGKHYAIAVFVKDSMESEEVNCGMIAQVSKIVWDALNKKK"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42889": {"category_aro_name": "CME beta-lactamase", "category_aro_cvterm_id": "42889", "category_aro_accession": "3004774", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CME is a class A beta-lactamase gene family belonging to Chryseobacterium meningosepticum."}}, "ARO_name": "CME-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42890", "model_name": "CME-1", "model_type_id": "40292"}, "3574": {"model_id": "3574", "ARO_accession": "3004773", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CKO-1 is a class A beta-lactamase gene found in Citrobacter koseri.", "model_sequences": {"sequence": {"5770": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAACGAGGAAGTCATTAGTATGTGGCAACGGATGAAATGGGGTCTGTGTGTGCTGGCGGCACTCAGCGGTTCTGCGATGGCCGCACCGCTGACGGCGCAATACGTGTCGGCTATCGCGATGCAGGAAGAACAGCGTCTTCATGCCCGGATTGGCATTGCGGTACTTGATACGGCGACCAACAGTATCACCCATTATCGGGGAGAAGAACGGTTCCCGTTAAACAGTACGCACAAGCCGCTGTTATGCGCAGCGTTATTACGCGAAGTCGACAGGAAGGCGCTGGCGCTTTCTGCTTCAATGCAGTTTGAACCCTCACAACTGGTGGAGTATTCGCCGATTACTGAAAAACATGTGGCGCCAGACGCCATGAGCTGGGCGCAATTGTGCAGCGCGGCGGTAAGCTACAGCGATAACACGGCCGCCAATCTCATCGCCAGGAAGCTCAACGGGCCGCAGGCCGTCACGCAGTTTTTGCGTGATTCGGGGGATACGATAACCCGCCTCGATCGCTATGAGCCCGAACTGAACAGCGCCATTCCCGGTGATGAACGCGACTCCACGACGCCTGTCGCGATAGCGCAGACGCTCAATACGCTACTGCTGGGGAACGTGTTGCAGCCATCCTCAAGAGAGCAGCTTATGCAATGGATGCGGGACGACAAAGTGGCCGACGGTCTGCTGCGTTCGGTCTTGCCGGACGGCTGGAAAATCGCGGATAAAACCGGGGCGGGCGACAACGGCTCGCGTTCTATTGTCAGCGTTGTCTGGCCGACATCACAAAAACCTTTGCTCGTGGTTATCTATATTACACAAACTCCGGCGACAATGGCGCAGCGTGACGCCGCGATTGTCCGTATCGGGGAGTCGCTGTTTTCAACACTCGCAGTCTATGATTAA", "fmax": "903", "accession": "AF477396.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Citrobacter koseri", "NCBI_taxonomy_id": "545", "NCBI_taxonomy_cvterm_id": "36934"}, "protein_sequence": {"accession": "AAL85333.1", "sequence": "MRNEEVISMWQRMKWGLCVLAALSGSAMAAPLTAQYVSAIAMQEEQRLHARIGIAVLDTATNSITHYRGEERFPLNSTHKPLLCAALLREVDRKALALSASMQFEPSQLVEYSPITEKHVAPDAMSWAQLCSAAVSYSDNTAANLIARKLNGPQAVTQFLRDSGDTITRLDRYEPELNSAIPGDERDSTTPVAIAQTLNTLLLGNVLQPSSREQLMQWMRDDKVADGLLRSVLPDGWKIADKTGAGDNGSRSIVSVVWPTSQKPLLVVIYITQTPATMAQRDAAIVRIGESLFSTLAVYD"}}}}, "ARO_category": {"42887": {"category_aro_name": "CKO beta-lactamase", "category_aro_cvterm_id": "42887", "category_aro_accession": "3004772", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CKO is a class A beta-lactamase gene family found in Citrobacter koseri."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "CKO-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42888", "model_name": "CKO-1", "model_type_id": "40292"}, "3577": {"model_id": "3577", "ARO_accession": "3003652", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From Lahey's list of beta-lactamases, no additional information available", "model_sequences": {"sequence": {"5775": {"dna_sequence": {"partial": "0", "sequence": "ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAAACTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA", "fmax": "1146", "accession": "KP862820.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AKZ20822.1", "sequence": "MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKKLGIVMLANKSYPNPVRVEAAWRILEKLQ"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36208": {"category_aro_name": "CMY beta-lactamase", "category_aro_cvterm_id": "36208", "category_aro_accession": "3000069", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins 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. The 7-alpha-methoxy group increases resistance to beta-lactamases."}}, "ARO_name": "CMY-132", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40262", "model_name": "CMY-132", "model_type_id": "40292"}, "3576": {"model_id": "3576", "ARO_accession": "3004777", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CMH-1 is a class C beta-lactamase gene found in Enterobacter cloacae.", "model_sequences": {"sequence": {"5772": {"dna_sequence": {"partial": "0", "sequence": "ATGATGACAAAATCCCTAAGCTGCGCGCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCTCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGTGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAACCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGTTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA", "fmax": "1146", "accession": "JQ673557.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "AFI56422.1", "sequence": "MMTKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMCFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42891": {"category_aro_name": "CMH beta-lactamase", "category_aro_cvterm_id": "42891", "category_aro_accession": "3004776", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae."}}, "ARO_name": "CMH-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42892", "model_name": "CMH-1", "model_type_id": "40292"}, "3571": {"model_id": "3571", "ARO_accession": "3004769", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CIA-2 is a class A beta-lactamase gene found in Chryseobacterium indologenes.", "model_sequences": {"sequence": {"5767": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACATTTCTTATACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACGGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATGAGAAGCTGCCGTTACTCAGCGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACAGATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGATCTTCAGATCAAATATAATGAGGACGACATGCACAGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGGAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAGGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTGCTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCCAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA", "fmax": "879", "accession": "AB674566.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Chryseobacterium indologenes", "NCBI_taxonomy_id": "253", "NCBI_taxonomy_cvterm_id": "36916"}, "protein_sequence": {"accession": "BAL40893.1", "sequence": "MKKITFLILMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDEKLPLLSVFKFHLACAVLDMADKGKFSTDQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLGTTTGTNKIVEQLPKGTPVAHKTGSSGKPDNILAVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "42881": {"category_aro_name": "CIA beta-lactamase", "category_aro_cvterm_id": "42881", "category_aro_accession": "3004767", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes."}}, "ARO_name": "CIA-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42884", "model_name": "CIA-2", "model_type_id": "40292"}, "3570": {"model_id": "3570", "ARO_accession": "3004768", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CIA-1 is a class A beta-lactamase gene found in Chryseobacterium indologenes.", "model_sequences": {"sequence": {"5766": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACATTTCTTTTACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACCGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATAAGAAACTGCCGTTACTCAGTGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACAGATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGACCTTCAGATCAAATATAATGAGGACGACATGCACAGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGGAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAAGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTACTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCTAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA", "fmax": "879", "accession": "AB639753.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Chryseobacterium indologenes NBRC 14944", "NCBI_taxonomy_id": "1218103", "NCBI_taxonomy_cvterm_id": "42883"}, "protein_sequence": {"accession": "BAL40892.1", "sequence": "MKKITFLLLMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDKKLPLLSVFKFHLACAVLDMADKGKFSTDQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLGTTTGTNKIVEQLPKSTPVAHKTGSSGKPDNILTVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "42881": {"category_aro_name": "CIA beta-lactamase", "category_aro_cvterm_id": "42881", "category_aro_accession": "3004767", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes."}}, "ARO_name": "CIA-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42882", "model_name": "CIA-1", "model_type_id": "40292"}, "3573": {"model_id": "3573", "ARO_accession": "3004771", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CIA-4 is a class A beta-lactamase gene found in Chryseobacterium indologenes.", "model_sequences": {"sequence": {"5769": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACATTTCTTATACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACGGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATGAGAAGCTGCCGTTACTCAGCGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACAGATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGATCTTCAGATCAAATATAATGAGGACGACATGCACAGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGGAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAGGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTACTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCCAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA", "fmax": "879", "accession": "AB674568.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Chryseobacterium indologenes", "NCBI_taxonomy_id": "253", "NCBI_taxonomy_cvterm_id": "36916"}, "protein_sequence": {"accession": "BAL40895.1", "sequence": "MKKITFLILMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDEKLPLLSVFKFHLACAVLDMADKGKFSTDQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLGTTTGTNKIVEQLPKGTPVAHKTGSSGKPDNILTVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "42881": {"category_aro_name": "CIA beta-lactamase", "category_aro_cvterm_id": "42881", "category_aro_accession": "3004767", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes."}}, "ARO_name": "CIA-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42886", "model_name": "CIA-4", "model_type_id": "40292"}, "3572": {"model_id": "3572", "ARO_accession": "3004770", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CIA-3 is a class A beta-lactamase gene found in Chryseobacterium indologenes.", "model_sequences": {"sequence": {"5768": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACATTTCTTTTACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACGGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATGAGAAGCTGCCGTTACTCAGCGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACATATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGATCTTCAGATCAAATATAATGAGGACGACATGCACCGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGCAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAGGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTACTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCCAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA", "fmax": "879", "accession": "AB674567.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Chryseobacterium indologenes", "NCBI_taxonomy_id": "253", "NCBI_taxonomy_cvterm_id": "36916"}, "protein_sequence": {"accession": "BAL40894.1", "sequence": "MKKITFLLLMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDEKLPLLSVFKFHLACAVLDMADKGKFSTYQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLATTTGTNKIVEQLPKGTPVAHKTGSSGKPDNILTVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "42881": {"category_aro_name": "CIA beta-lactamase", "category_aro_cvterm_id": "42881", "category_aro_accession": "3004767", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes."}}, "ARO_name": "CIA-3", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42885", "model_name": "CIA-3", "model_type_id": "40292"}, "3479": {"model_id": "3479", "ARO_accession": "3001533", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-345 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5673": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF048918.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AHN07463.1", "sequence": "MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-345", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37933", "model_name": "OXA-345", "model_type_id": "40292"}, "3592": {"model_id": "3592", "ARO_accession": "3004797", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-1 is a carbapenem-hydrolyzing Class A beta-lactamase found in Enterobacter cloacae.", "model_sequences": {"sequence": {"5790": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTTAAAAAAGGTGCAAGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGTAATTAATAGTGTTGAGGAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACCCAAAAAATGGGAAAGAATTTGCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACTCAGGAGAAATCTGTTTCTCTTGATGATATGGTGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGTAAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACACAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGACAGACGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAAATGCTGCAAAAATAGCTATAAAGGCAGTTTATGGAAGTTATAAATAA", "fmax": "4376", "accession": "KT192551.1", "fmin": "3491", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "ALE30770.1", "sequence": "MFFFKKGASTFIFLLCLPLNSFASQVINSVEEMRELETSFGGRIGVYILNPKNGKEFAYRQDERFPLCSSFKAFLAASVLKRTQEKSVSLDDMVEYSGRVMEKHSPVSEKYRKTGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNTAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDVAILWTDANSPAVMAVYTTRPNQNDKHDEAVIKNAAKIAIKAVYGSYK"}}}}, "ARO_category": {"42915": {"category_aro_name": "FRI beta-lactamase", "category_aro_cvterm_id": "42915", "category_aro_accession": "3004796", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "FRI-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42916", "model_name": "FRI-1", "model_type_id": "40292"}, "3580": {"model_id": "3580", "ARO_accession": "3004780", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "DES-1 is a class A beta-lactamase gene found in Desulfovibrio desulfuricans.", "model_sequences": {"sequence": {"5778": {"dna_sequence": {"partial": "0", "sequence": "ATGCATTCCCGTTCCAGTTATTCCAGGCGCTATGTGCTCGCGGGCCTGTGCGCCCTGCCTTTTGCCTCGCTGAGCGCAGGCCTTATTTTCAACAGCTCTGCTGATGCCGCCTCTCTTGCTGCAATTAACGGAAAAACCCTGCAAAAAAAGCTGGCCGAACTTGAGGCCGCAAGCGGCGGCAGGCTTGGCGTGGCTGCCCGGTCAAGCAATGGCGGCAAAAGCCTGTCTTACCGTGGGGACGAACGCTTTCCCATGTGCAGCACCTTTAAAGTGCTGGCAGTTGCGGCCCTTCTGCGGGACAAACCGGGCATTCTTGAACAGAGAATCCACTTTGCCCAAATCGACATCCAGCCCTGGTCGCCCGTTACAGAAAAGCACCTTGAAGACGGCATGACTGTGGCAGAATTGTGCGCCGCCATGCTCCAGCACAGCGACAACACGGCTGCCAACCTTGTGCTTGCCAAACTGGGCGGCCCGCAAGGCCTGACCTCCCTTGCCCGCAGTTTTGGCGACACAACGTTTCGCCTTGACCGCTGGGAAGTGGAACTGAATACGGCCATCCCCGGCGATGCGCGCGACACCACAACGCCCCTGGCCATGTGCAACACCCTGAACGGATTGCTGTGTGGCAACCTGCTGAAAGCGCCCGCACGCGAACGACTGACAGGCTGGATGCTGGGCTGCGCAACCGGGGCCGGGCGCATCCCCGCAGGAATTCCGCAGGGCTGGCGCTCTGCGCACAAAAGCGGCAGCGGAGAAAACGGCACCGCCAATGATGTAGGAGTATTGCTGCCGCCGAGCAACCCTGGCAAAGCCACAAAGCCCGGCAAGAACAAAGGCAAGCCGCTGACTGTGGCCCTCTACCTCACGGGATCGCGACTGACCGGGCCGGAAAACGACAAAATCCTTGCCAGTGCAACCCGCCTGGTCTGCGCCGCAGAAGGGCTTGCGATGCCGCTCGACAATATGTATTGA", "fmax": "1093", "accession": "AF426161.1", "fmin": "118", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Desulfovibrio desulfuricans", "NCBI_taxonomy_id": "876", "NCBI_taxonomy_cvterm_id": "42896"}, "protein_sequence": {"accession": "AAM45855.1", "sequence": "MHSRSSYSRRYVLAGLCALPFASLSAGLIFNSSADAASLAAINGKTLQKKLAELEAASGGRLGVAARSSNGGKSLSYRGDERFPMCSTFKVLAVAALLRDKPGILEQRIHFAQIDIQPWSPVTEKHLEDGMTVAELCAAMLQHSDNTAANLVLAKLGGPQGLTSLARSFGDTTFRLDRWEVELNTAIPGDARDTTTPLAMCNTLNGLLCGNLLKAPARERLTGWMLGCATGAGRIPAGIPQGWRSAHKSGSGENGTANDVGVLLPPSNPGKATKPGKNKGKPLTVALYLTGSRLTGPENDKILASATRLVCAAEGLAMPLDNMY"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42894": {"category_aro_name": "DES beta-lactamase", "category_aro_cvterm_id": "42894", "category_aro_accession": "3004779", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "DES is a class A beta-lactamase gene family found in Desulfovibrio desulfuricans."}}, "ARO_name": "DES-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42895", "model_name": "DES-1", "model_type_id": "40292"}, "3581": {"model_id": "3581", "ARO_accession": "3002140", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "DHA-9 is a beta-lactamase. From the Lahey list of DHA beta-lactamases.", "model_sequences": {"sequence": {"5779": {"dna_sequence": {"partial": "1", "sequence": "ATGACAAAATCTGTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCAGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCATTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA", "fmax": "2091", "accession": "KJ207201.1", "fmin": "951", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Morganella morganii", "NCBI_taxonomy_id": "582", "NCBI_taxonomy_cvterm_id": "36917"}, "protein_sequence": {"accession": "AHL39320.1", "sequence": "MTKSVSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSHYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins 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. The 7-alpha-methoxy group increases resistance to beta-lactamases."}, "36207": {"category_aro_name": "DHA beta-lactamase", "category_aro_cvterm_id": "36207", "category_aro_accession": "3000068", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins."}}, "ARO_name": "DHA-9", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38540", "model_name": "DHA-9", "model_type_id": "40292"}, "3582": {"model_id": "3582", "ARO_accession": "3004782", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ERP-1 is a class A beta-lactamase gene found in Erwinia persicina.", "model_sequences": {"sequence": {"5780": {"dna_sequence": {"partial": "0", "sequence": "ATGACGATTTTACTGCAACGCCGCCAGCTTCTGGTGGCGGGCGCGGCGCTGGCGCTGACCGCCTCGCTGACACCACTGAACGTATTTGCAGCAGGTGACTCGCTGCAGCGGCAGCTTGCCGCACTGGAAACGGAGGTGAATGGCCGTATCGGGCTGTCTCTGATCGACAGCGCCAGCCAGCAGGCGTGGAGCTATCGCGGTGACGAACGCTTTCCGCTGTGCAGCACCTTTAAACTGCTGCTGGTGGCTGCCGTTTTAAAACGCAGCGAGTCACAGCCCGCCCTGATGCAACAAACCCTGCACTGGACACCTGCGGATCACCTGAGCTATATGCCGGTAACGGCGAAGCATCCGCAGGGGATGACCGTCAGCGATCTGTGTGCAGCCGCGCTGCAGTACAGTGATAACCTGGCGGCCAACGTACTGTTGACACTGCTGGGGGGACCCGCGTCGGTGACCCGGCTGGCCCGCTCTTTAGGTGACAGTGTCACGCAGCTCGATCGTAATGAACCGACACTGAATACCGCGATCCCGGGCGATCCGCGTGACACCACCACGCCGCTGCACATGTCGCACAGCGTGCAGCAGTTGCTGGTGAAGTCGGGATTACAGACAGCACAGCAGCAGCAGCTGATCGCCTGGCTGAAGGGGAACACCACAGGGAAAAACGCCATTGCCGCAGCGCTGCCTGCGGGCTGGGAAATCGGGGATAAGACCGGCAGCGGGGGCTATGGCACAACCAACGATGTCGCCATCCTCTGGCCTCCGGGCAAGGCTCCGCTGATCCTGGCCATCTATTTTACCCAGCATGCCCCGGAGGCGAAGAGTCGTCAGGACGTGCTGGCGAAAGCGGCCGCCATTGCACTGAAATCTGTTATCTGA", "fmax": "882", "accession": "AY077733.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Erwinia persicina", "NCBI_taxonomy_id": "55211", "NCBI_taxonomy_cvterm_id": "42899"}, "protein_sequence": {"accession": "AAL86999.1", "sequence": "MTILLQRRQLLVAGAALALTASLTPLNVFAAGDSLQRQLAALETEVNGRIGLSLIDSASQQAWSYRGDERFPLCSTFKLLLVAAVLKRSESQPALMQQTLHWTPADHLSYMPVTAKHPQGMTVSDLCAAALQYSDNLAANVLLTLLGGPASVTRLARSLGDSVTQLDRNEPTLNTAIPGDPRDTTTPLHMSHSVQQLLVKSGLQTAQQQQLIAWLKGNTTGKNAIAAALPAGWEIGDKTGSGGYGTTNDVAILWPPGKAPLILAIYFTQHAPEAKSRQDVLAKAAAIALKSVI"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42897": {"category_aro_name": "ERP beta-lactamase", "category_aro_cvterm_id": "42897", "category_aro_accession": "3004781", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ERP is a class A beta-lactamase gene family found in Erwinia persicina."}}, "ARO_name": "ERP-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42898", "model_name": "ERP-1", "model_type_id": "40292"}, "3583": {"model_id": "3583", "ARO_accession": "3004784", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FAR-1 is a class A beta-lactamase gene found in Nocardia farcinica.", "model_sequences": {"sequence": {"5781": {"dna_sequence": {"partial": "0", "sequence": "ATGGCGGCCGCCGCGGCGATCGCGCTACTGGGCGGCTGCGGCGCGGACGCGGGTTCCGAGCCCGCCACCACCGCGGCGAGCACGACCGCGCCGAGCACGGCCACCGACGCGGCGACCGCCGAGTTCGCCGCACTGGAACAGCGATCCGGCGCGCGGCTGGGCGTCTACGCGGTCGACACGACCAGCGGCGCCGAGGTCGCCTACCGGGCGGACGAGCGGTTCGGCATGGCCTCCACCTTCAAGGGCCTGGCCTGCGGCGCGCTGCTGCGCGAGCACCCGCTGTCGTCCGGCTATTTCGACCAGGTCGTCCGCTACTCCCGCGAGGAGGTGGTGTCCTATTCGCCGGTCACCGAGACCCGCGTGGACACCGGGATGACCGTCGCCGAACTGTGCCACGCCACGATCACCGTCAGCGACAACACCGCGGGCAACCAGATCCTGAAACTGCTCGGCGGCCCCGCCGGTTTCACCGCCTTCCTGCGCTCGCTCGGCGACGAGGTGAGCCGGCTGGACCGCTGGGAGACCGAACTCAACGAGGTGCCGCCCGGCGAGGAACGCGACACCACCACCCCCGCCGCCGTGGCGGCGAACTACCGCGCGCTGGTGCTCGGTGACGTGCTCGCCGAGCCCGAGCGCGCCCAGTTGCGGGACTGGCTGGTCGCCAACACCACCGGCGACCAGCGCATCCGTGCGGGCGTGCCCGCGGGCTGGACGGTCGGCGACAAGACCGGCGGCGGCAGCCACGGCGGCAACAACGACGTGGCCGTGGCCTGGACCGAGACCGGCGACCCGATCGTCATCGCCCTGCTCTCGCACCGCACCGACCCCGCCGCCAAGGCCGACAACGCCCTGCTCGCCGAGGCGACCCGGGCGGTGGTCACCGCCCTGCGATGA", "fmax": "1196", "accession": "AF024601.1", "fmin": "302", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Nocardia farcinica", "NCBI_taxonomy_id": "37329", "NCBI_taxonomy_cvterm_id": "42902"}, "protein_sequence": {"accession": "AAB81957.1", "sequence": "MAAAAAIALLGGCGADAGSEPATTAASTTAPSTATDAATAEFAALEQRSGARLGVYAVDTTSGAEVAYRADERFGMASTFKGLACGALLREHPLSSGYFDQVVRYSREEVVSYSPVTETRVDTGMTVAELCHATITVSDNTAGNQILKLLGGPAGFTAFLRSLGDEVSRLDRWETELNEVPPGEERDTTTPAAVAANYRALVLGDVLAEPERAQLRDWLVANTTGDQRIRAGVPAGWTVGDKTGGGSHGGNNDVAVAWTETGDPIVIALLSHRTDPAAKADNALLAEATRAVVTALR"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42900": {"category_aro_name": "FAR beta-lactamase", "category_aro_cvterm_id": "42900", "category_aro_accession": "3004783", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FAR is a class A extended spectrum beta-lactamase gene family found in Nocardia farcinica."}}, "ARO_name": "FAR-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42901", "model_name": "FAR-1", "model_type_id": "40292"}, "3584": {"model_id": "3584", "ARO_accession": "3004786", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FIM-1 is a metallo-beta-lactamase gene found in Pseudomonas aeruginosa from isolates in Italy.", "model_sequences": {"sequence": {"5782": {"dna_sequence": {"partial": "1", "sequence": "ATGCGCCCCTTACCCCATTCATACCTAAAGAGTCTTGTCATTTGCCTGCTGACGGCCTTCGCCGCCTTAACACCCGTCGTGAACTCTGGCGTACAAGCGGCTCAACCCAAAGACGTGCCGGTAACGTTTACCGCTATTACGCAGGGGGTGTGGATGCACACCAGCATGAAGCACATGGAAAACTGGGGGCATGTACCCAGTAACGGGCTAATCGTTGAAAAAGGAGACTTTAGTATTTTGGTGGATACGGCTTGGGACGATCCACAAACGGCACAGATTATTGAGTGGTCCAAAGATACGCTAAAAAAACCCATTCGTTGGGCGGTGTTTACCCATGCCCACGACGACAAAATGGGCGGGGTGGCTGCCTTACGACAGCAGGGCATTGTGACCTATGCGGCGGCCGACTCTAATCGAATGGCCCCACAGAATGGCTTAACCCCTGCAGAGCATGACCTCATCTTTGATAGCGAGCACAGCACAAGCGTTCTGCATCCGCTGGTCATTTTCGATCCCGGCCCAGGGCATACCCGCGACAATATTGTGGTGGGCCTGCCCGAGCAAGGGATTGTTTTTGGAGGCTGTCTCATTCGCCCATCGGGCAGCACGTCTCTGGGAAACACCGCTGACGCCGATCTCGCTCACTGGAAAACAGCGGTATTGGCCGTTGCGCAGCGCTTTGCGGAGGCCCAACAGATTATACCCAGCCACGGACCCATGGCCGGACGAGAGCTTTTTGAACTGACGGCTCAGCTGGCAGAAAAGGCCAGCATACCGTCCACACCCTGA", "fmax": "2725", "accession": "JX570731.1", "fmin": "1936", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AFV91534.1", "sequence": "MRPLPHSYLKSLVICLLTAFAALTPVVNSGVQAAQPKDVPVTFTAITQGVWMHTSMKHMENWGHVPSNGLIVEKGDFSILVDTAWDDPQTAQIIEWSKDTLKKPIRWAVFTHAHDDKMGGVAALRQQGIVTYAAADSNRMAPQNGLTPAEHDLIFDSEHSTSVLHPLVIFDPGPGHTRDNIVVGLPEQGIVFGGCLIRPSGSTSLGNTADADLAHWKTAVLAVAQRFAEAQQIIPSHGPMAGRELFELTAQLAEKASIPSTP"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42903": {"category_aro_name": "FIM beta-lactamase", "category_aro_cvterm_id": "42903", "category_aro_accession": "3004785", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FIM is a metallo-beta-lactamase gene family found in Pseudomonas aeruginosa."}}, "ARO_name": "FIM-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42904", "model_name": "FIM-1", "model_type_id": "40292"}, "3585": {"model_id": "3585", "ARO_accession": "3004788", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FONA-1 is a class A beta-lactamase gene found in Serratia fonticola.", "model_sequences": {"sequence": {"5783": {"dna_sequence": {"partial": "0", "sequence": "ATGATTAAAAATACACTACGTAAAACCACCCTGATGGTGGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAGCTGGAGAAAAGCTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAAATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTAACAGAATTTGCGCGTACCATCGGCGATAAAACCTTCCGTCTTGATCGTACCGAGCCCACCTTGAATACCGCCATTCCGGGTGATGAACGTGACACGAGTTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAGGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGATAGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTTACCGAAGGGCTTTGA", "fmax": "1941", "accession": "AJ251239.1", "fmin": "1053", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia fonticola", "NCBI_taxonomy_id": "47917", "NCBI_taxonomy_cvterm_id": "39675"}, "protein_sequence": {"accession": "CAB61635.1", "sequence": "MIKNTLRKTTLMVATVMPLLFGSAPLWAQTANAKANIQQQLSELEKSSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDERDTSSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWIVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42905": {"category_aro_name": "FONA beta-lactamase", "category_aro_cvterm_id": "42905", "category_aro_accession": "3004787", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FONA is a class A beta-lactamase gene family found in Serratia fonticola."}}, "ARO_name": "FONA-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42906", "model_name": "FONA-1", "model_type_id": "40292"}, "3586": {"model_id": "3586", "ARO_accession": "3004789", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FONA-2 is a class A beta-lactamase gene found in Serratia fonticola.", "model_sequences": {"sequence": {"5784": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAATACACTACGTAAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCAGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTAACAGAATTTGCGCGTACCATCGGCGATAAAACCTTCCGTCTTGATCGTACCGAGCCCACCTTGAATACCGCCATTCCGGGTGATCCGCGTGACACGAGTTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGTAAGGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGATAGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGCTGGTCACCTATTTCACCCAGCCACAGCAGAATGCTGAAGCCCGCAAAGACGTGTTGGCTGCGGCCGCTAAAATTGTTACCGAAGGGCTTTGA", "fmax": "1941", "accession": "AJ251240.1", "fmin": "1053", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia fonticola", "NCBI_taxonomy_id": "47917", "NCBI_taxonomy_cvterm_id": "39675"}, "protein_sequence": {"accession": "CAB61637.1", "sequence": "MVKNTLRKTTLMVATVMPLLFSSAPLWAQTANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDPRDTSSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWIVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42905": {"category_aro_name": "FONA beta-lactamase", "category_aro_cvterm_id": "42905", "category_aro_accession": "3004787", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FONA is a class A beta-lactamase gene family found in Serratia fonticola."}}, "ARO_name": "FONA-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42907", "model_name": "FONA-2", "model_type_id": "40292"}, "3587": {"model_id": "3587", "ARO_accession": "3004790", "model_param": {"blastp_bit_score": {"param_value": "585", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FONA-3 is a class A beta-lactamase gene found in Serratia fonticola.", "model_sequences": {"sequence": {"5785": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAATATACTACGTAAAACCACCCTGATGGTCACTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCTTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATTGGCGATAAAACCTTCCGCCTCGATCGTACCGAACCCACTTTAAATACCGCCATTCCAGGTGATAAGCGTGATACCACCTCACCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACTACATGGGTGGTTGGGGATAAAACCGGCAGCGGTGATTATGGTACCACTAACGATATCGCCGTTATTTGGCCAGCGAACCACGCGCCGTTGGTGTTAGTAACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCTCGTAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTTACCGAAGGGCTTTGA", "fmax": "1941", "accession": "AJ251241.1", "fmin": "1053", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia fonticola", "NCBI_taxonomy_id": "47917", "NCBI_taxonomy_cvterm_id": "39675"}, "protein_sequence": {"accession": "CAB61639.1", "sequence": "MVKNILRKTTLMVTTVMPLLFGSAPLWAQTANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42905": {"category_aro_name": "FONA beta-lactamase", "category_aro_cvterm_id": "42905", "category_aro_accession": "3004787", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FONA is a class A beta-lactamase gene family found in Serratia fonticola."}}, "ARO_name": "FONA-3", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42908", "model_name": "FONA-3", "model_type_id": "40292"}, "3588": {"model_id": "3588", "ARO_accession": "3004791", "model_param": {"blastp_bit_score": {"param_value": "585", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FONA-4 is a class A beta-lactamase gene found in Serratia fonticola.", "model_sequences": {"sequence": {"5786": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAATACACTACGTAAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGTTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAGCTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTAACAGAATTTGCGCGTACCATCGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACCTTGAATACCGCCATTCCGGGTGATGAACGTGACACGAGTTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAGGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGAGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGATAGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACCCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCCGCTAAAATTGTTACCGAAGGGCTTTGA", "fmax": "1941", "accession": "AJ251242.1", "fmin": "1053", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia fonticola", "NCBI_taxonomy_id": "47917", "NCBI_taxonomy_cvterm_id": "39675"}, "protein_sequence": {"accession": "CAB61641.1", "sequence": "MVKNTLRKTTLMVATVMPLLFGSAPLWAQTANAKANIQQQLSELEKSSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDERDTSSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWIVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42905": {"category_aro_name": "FONA beta-lactamase", "category_aro_cvterm_id": "42905", "category_aro_accession": "3004787", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FONA is a class A beta-lactamase gene family found in Serratia fonticola."}}, "ARO_name": "FONA-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42909", "model_name": "FONA-4", "model_type_id": "40292"}, "3589": {"model_id": "3589", "ARO_accession": "3004792", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FONA-5 is a class A beta-lactamase gene found in Serratia fonticola.", "model_sequences": {"sequence": {"5787": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAGAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGTTATGGGCGCAACCCGCTAATGCCAAGGCCAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGTGGGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAACAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACTATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATCGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCCATCCCGGGTGATAAGCGTGACACCACCTCGCCGCAGGCGATGGCAATAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTTGCTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGGTGGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTCACCGAAGGGCTTTGA", "fmax": "1941", "accession": "AJ251243.1", "fmin": "1053", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia fonticola", "NCBI_taxonomy_id": "47917", "NCBI_taxonomy_cvterm_id": "39675"}, "protein_sequence": {"accession": "CAB61643.1", "sequence": "MVRNTLRQTTLMVATVMPLLFGSAPLWAQPANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPQAMAISLQNLTLGKALAEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42905": {"category_aro_name": "FONA beta-lactamase", "category_aro_cvterm_id": "42905", "category_aro_accession": "3004787", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FONA is a class A beta-lactamase gene family found in Serratia fonticola."}}, "ARO_name": "FONA-5", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42910", "model_name": "FONA-5", "model_type_id": "40292"}, "3519": {"model_id": "3519", "ARO_accession": "3003606", "model_param": {"blastp_bit_score": {"param_value": "514", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5714": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGACTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG", "fmax": "774", "accession": "KR061502.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter coli", "NCBI_taxonomy_id": "195", "NCBI_taxonomy_cvterm_id": "36835"}, "protein_sequence": {"accession": "AKI29914.1", "sequence": "MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRTMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-450", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40216", "model_name": "OXA-450", "model_type_id": "40292"}, "3518": {"model_id": "3518", "ARO_accession": "3003605", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5713": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCATCTTGTTTTTATGGATTTTAAATTTTGCCTTTGGACAAGATAAAATATTAGAAGATTTTTTTAAAGATTATAATACAAGTGGGATTTTTATAATCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCAAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCCAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGCACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA", "fmax": "750", "accession": "KR061498.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29910.1", "sequence": "MKKIILFLWILNFAFGQDKILEDFFKDYNTSGIFIIFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKHIKNIKIREELLEKYLAIITN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-449", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40215", "model_name": "OXA-449", "model_type_id": "40292"}, "3591": {"model_id": "3591", "ARO_accession": "3004795", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FPH-1 is a carbapenem-hydrolyzing class A beta-lactamase gene found in Francisella philomiragia.", "model_sequences": {"sequence": {"5789": {"dna_sequence": {"partial": "0", "sequence": "ATGAAACGTTTATTATTTACATCTTTATACTTAATTCCAACATTTTTACTAGCAAACACTACTCTAGATGACTCTTTTAAGAATCTGGAAGATGAATATCATGGTAAACTCGGTATATACACCCTCAATACAGATGATAAAACTAATATCAGCTACAATGAAAATTATCACTTCCCAATTTGTAGTGTTTTTAAATTTTTATTAGTTGGTGCAGTTCTAGAATATGATATGCAACACAAAGGTTTTTTAGATAAAAAAATTCTAATAACTCAAGACGATATTGGTACTCTAGGTTATGCTCCAGTAACAGGCAAAAATATTGGTAAAACTTTGACAATATCACAGCTCAATTACGCAGCTATTCTAAGTGATAATCCTGCTGCTAATATCCTTGTTAGAGAGATTGGGGGCTTGGAAAAGCTTAATAAATTAGTAGCAAAACTAGGAGATAAAGATACTATTATCAAAAATGATGAACCTAAAATCAATCATACAAAGCCAGATAGTAATATCAACAAAACAACGCCCAAAGCTATAACTCAAGATATCTATAATCTAGCATTTGGTAATATTTTGGATAAAAAACATCGTGAAATCTTCATAGGATATTTACAAAAAAACAATACTGGTGCAAATAGAATAGCGTATAGTATGCCTAAAAATTGGACAATTGGTGATAAGACAGGAACTTGTGGAGAGTATGCGGCTACTAATGATGTAGCTATAATTTGGCCACAGAATAAACCGCCTTTTGCTCTAAGTATTCTATATACAAACCCTAGTGATGTAAAAGCTCCAAGTAATGAAAAAATTATTCAGCAAGCATCTAAGTTAGTTTCAGAAAGTATAGCTAAGAAAGATTCTTAA", "fmax": "79185", "accession": "CP010019.1", "fmin": "78318", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Francisella philomiragia subsp. philomiragia ATCC 25015", "NCBI_taxonomy_id": "539329", "NCBI_taxonomy_cvterm_id": "42914"}, "protein_sequence": {"accession": "AJI75632.1", "sequence": "MKRLLFTSLYLIPTFLLANTTLDDSFKNLEDEYHGKLGIYTLNTDDKTNISYNENYHFPICSVFKFLLVGAVLEYDMQHKGFLDKKILITQDDIGTLGYAPVTGKNIGKTLTISQLNYAAILSDNPAANILVREIGGLEKLNKLVAKLGDKDTIIKNDEPKINHTKPDSNINKTTPKAITQDIYNLAFGNILDKKHREIFIGYLQKNNTGANRIAYSMPKNWTIGDKTGTCGEYAATNDVAIIWPQNKPPFALSILYTNPSDVKAPSNEKIIQQASKLVSESIAKKDS"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42912": {"category_aro_name": "FPH beta-lactamase", "category_aro_cvterm_id": "42912", "category_aro_accession": "3004794", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FPH is a carbapenem-hydrolyzing class A beta-lactamase found in Francisella philomiragia."}}, "ARO_name": "FPH-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42913", "model_name": "FPH-1", "model_type_id": "40292"}, "3508": {"model_id": "3508", "ARO_accession": "3003594", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5703": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATATGGATACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG", "fmax": "792", "accession": "KP410734.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AKL59521.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-438", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40204", "model_name": "OXA-438", "model_type_id": "40292"}, "3509": {"model_id": "3509", "ARO_accession": "3003595", "model_param": {"blastp_bit_score": {"param_value": "525", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5704": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTCATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG", "fmax": "786", "accession": "KP727573.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AKR53961.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVHQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-439", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40205", "model_name": "OXA-439", "model_type_id": "40292"}, "3465": {"model_id": "3465", "ARO_accession": "3001758", "model_param": {"blastp_bit_score": {"param_value": "570", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-303 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5660": {"dna_sequence": {"partial": "0", "sequence": "ATGATGATGTCGAAAAAATTAAAATGTCTGGCCTTTTTTACAGCCATCTTTTTTGCAATTCCCATGACTGCTTGTCAAAGTTTTAGCCAACAAAAGCAACAGCTCTCGACACAAAAAAATGAGCAGCAGCAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAATGGTGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAAATTTGGCAATGATCTTGATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGTTAAACGCCTTGATCGGAATACAGCATCATAAGACCACACCAGATGAAGTATTTAAATGGGATGGTAAAAAGCGGGCATTCAGCAGTTGGGAAAAAGACCTCACATTAGCTGAGGCGATGCAGGCATCGGCGGTACCCGTGTATCAAGAATTGGCAAGACGTATTGGTTTGGAACTGATGACCCGTGAAGTAAAGCGTGTGGGTTATGGTAATAAAAATATCGGGACACAAGTCGATAATTTCTGGTTAGTTGGCCCCTTAAAAATCACTCCCATAGAAGAAGTTCGCTTTGCCTATGCGCTGGCAAAACAGAAATTGCCCTTTGACCAGCCGACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACCAAAATCTATGCCAAAAGTGGTTGGGGTATGGATGTCAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGCAAGATCACAGCCTTCTCACTGAATATGCAAATGAGTCAGCCTGAACATGCAGATGCACGCAAAGTGATTGTGTATCAAGCCTTGCAAGAGTTGGGATTGTTAGCCCATTAA", "fmax": "195335", "accession": "APSD01000035.1", "fmin": "194492", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. ANC 3880", "NCBI_taxonomy_id": "1217701", "NCBI_taxonomy_cvterm_id": "42824"}, "protein_sequence": {"accession": "ENX56371.1", "sequence": "MMMSKKLKCLAFFTAIFFAIPMTACQSFSQQKQQLSTQKNEQQQISSLFQSAQTNGVLVIYDGKKIQKFGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPIEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKVIVYQALQELGLLAH"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-303", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38158", "model_name": "OXA-303", "model_type_id": "40292"}, "3464": {"model_id": "3464", "ARO_accession": "3001757", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-302 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5659": {"dna_sequence": {"partial": "0", "sequence": "ATGATGATGTCGAAAAAATTAAAATGTCTAGCGCTTCTTACACCCTGCATATTGATTCTTCAATTGACTGCTTGTCAAAGTGTTAGCCAGCAAAAGCAACAGCTTTCGACACAAACAAATGAACAGCAACAGATTTCAAGCTTATTTCAAAGTGCCCAAACCAAGGGAGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAGTTATGGCAATGATCTTAATCGTGCAGAGCAACGTTATATTCCTGCTTCGACCTTTAAAATCTTAAACGCCTTGATTGGCATACAGTATCATAAGACCACACCAAATGAAGTGTTTAAATGGGATGGTAAAAAGCGGACTTTCAGCAGCTGGGAAAAAGATTTAAGCCTAGCTGAAGCCATGCAGGCATCGGCTGTACCTGTCTATCAGGAGCTAGCACGACGGATTGGTCTAGAACTTATGACCCGTGAGGTGAAGCGTGTGGGCTATGGCAATAAAAATATTGGCACCCAAGTCGATAATTTTTGGTTGGTCGGGCCTTTGCAAATTACACCTGTAGAAGAAGTTCGATTCGTTTATGCATTAGCAAAGCAAAAACTACCATTTGACCAGTCAACTCAACAACAAGTGAAAGGTATGTTATTGGCAGATGAGCGTCAGGGGACCAAGATTTATGCCAAGAGCGGTTGGGGCATGGACGTTAGCCCACAGGTTGGATGGTGGACCGGCTGGATTGAACAGCCAAATGGCAAAACCATTGCATTTTCACTGAATATGCAAATGAGTCAGCCTGAGCATGCAAATGCGCGTAAAGTGATTGTTTATCAAGCATTGCAAGAATTGGGATTGTTAGCGAATTAA", "fmax": "77370", "accession": "APRT01000004.1", "fmin": "76527", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. CIP 64.2", "NCBI_taxonomy_id": "1217694", "NCBI_taxonomy_cvterm_id": "42823"}, "protein_sequence": {"accession": "ENX18112.1", "sequence": "MMMSKKLKCLALLTPCILILQLTACQSVSQQKQQLSTQTNEQQQISSLFQSAQTKGVLVIYDGKKIQSYGNDLNRAEQRYIPASTFKILNALIGIQYHKTTPNEVFKWDGKKRTFSSWEKDLSLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLQITPVEEVRFVYALAKQKLPFDQSTQQQVKGMLLADERQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKTIAFSLNMQMSQPEHANARKVIVYQALQELGLLAN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-302", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38157", "model_name": "OXA-302", "model_type_id": "40292"}, "3463": {"model_id": "3463", "ARO_accession": "3001756", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-301 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5658": {"dna_sequence": {"partial": "0", "sequence": "ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCTGTATATCAAGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA", "fmax": "22158", "accession": "APQG01000050.1", "fmin": "21327", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter bereziniae LMG 1003 = CIP 70.12", "NCBI_taxonomy_id": "981324", "NCBI_taxonomy_cvterm_id": "42822"}, "protein_sequence": {"accession": "ENV90372.1", "sequence": "MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-301", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38156", "model_name": "OXA-301", "model_type_id": "40292"}, "3462": {"model_id": "3462", "ARO_accession": "3001755", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-300 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5657": {"dna_sequence": {"partial": "0", "sequence": "ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGGAAAAGCAACCAATACTGAAGTATTTCAGTGGAATGGTGAAAAGCGTGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAAGAGCTTGCTCGACGTATTGGCTTGAAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTAGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCTTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATAGAAAGTCGTGGTGACAGCAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA", "fmax": "256746", "accession": "APPK01000054.1", "fmin": "255915", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter bereziniae NIPH 3", "NCBI_taxonomy_id": "1217651", "NCBI_taxonomy_cvterm_id": "42821"}, "protein_sequence": {"accession": "ENV20093.1", "sequence": "MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNGKATNTEVFQWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLKLMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIESRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-300", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38155", "model_name": "OXA-300", "model_type_id": "40292"}, "3461": {"model_id": "3461", "ARO_accession": "3001754", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-299 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5656": {"dna_sequence": {"partial": "0", "sequence": "ATGAATCCCTTCACAAAATACTGTGCAATTTTATGCCCCATAATTTTTCTGGGCGCCTGCACAATATCCCCTTTTTCACACGATCAAGCGCATTCTGCCCATGCCAGCCAATTAACAGATGCAGCCACTATCCGCAATTTGTTTAATCAAGCCAATGTTCAGGGCGTGATTCTCATTAAAAGCGGCAATGATCTTCAAGCATATGGCAATGCGATACAGCGCGCAGATCAGCCATTTATACCGGCCTCCACGTTTAAAATGCTGAATGCCCTGATTGGCATTGAACACAACAAAACTTCCCCAGACGAAGTATTCAAATGGAATGGGGAAAAACGCAGCTTTCCAGCTTGGGAAAAAGATTTAACCTTAGCGCAGGCCATGACCGCCTCTGCCGTACCGGTATATCAAGAATTGGCGCACAGAATTGGCTTAGAGCTGATGCAAAATGAAGTGAAGCGGGTTCAATTTGGCAATGGCGATATTGGCGCTCAAGTCGATAATTTCTGGCTGATGGGCCCGCTTAAAATTACACCAAGGCAGGAAGTGCAATTTGCCGATCAGCTGTCCCACTTGCAATTGCCCTTTCGCAAAAGCACACAGCAACAAGTGATTCAAATGCTGTTTATTGAACAGATCGGCAGTAAAGCGCTCTATGCCAAAAGCGGCTGGGGCATGGATGTTGAGCCTCAAGTCGGCTGGTATACCGGCTGGGTTGAAGATGCTCAAGGCAAAACCACAGCCTTTTCACTCAACCTAGAAATGGATCAATCCACACCGGCATCTCTGCGTAAAGAGCTGGTGATCAGCAGCTTAAAGCAGCTCAAAATCCTATAA", "fmax": "31929", "accession": "APQD01000016.1", "fmin": "31095", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter bouvetii DSM 14964 = CIP 107468", "NCBI_taxonomy_id": "1120925", "NCBI_taxonomy_cvterm_id": "42820"}, "protein_sequence": {"accession": "ENV82218.1", "sequence": "MNPFTKYCAILCPIIFLGACTISPFSHDQAHSAHASQLTDAATIRNLFNQANVQGVILIKSGNDLQAYGNAIQRADQPFIPASTFKMLNALIGIEHNKTSPDEVFKWNGEKRSFPAWEKDLTLAQAMTASAVPVYQELAHRIGLELMQNEVKRVQFGNGDIGAQVDNFWLMGPLKITPRQEVQFADQLSHLQLPFRKSTQQQVIQMLFIEQIGSKALYAKSGWGMDVEPQVGWYTGWVEDAQGKTTAFSLNLEMDQSTPASLRKELVISSLKQLKIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-299", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38154", "model_name": "OXA-299", "model_type_id": "40292"}, "3460": {"model_id": "3460", "ARO_accession": "3001753", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-298 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5655": {"dna_sequence": {"partial": "0", "sequence": "GTGTTGTTCAATTTTATAGTCATGCCGAAAAAATTAAAATTACTCGCTCTATCTGTAGTTGTGATGCCCTCAATAATATTATTGGGCTGCCAAAATATTCAGCCACACGTTCAAGCTTTAGTCACACAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTCACCTATGATGGCAAAGCTATTCAAAAATATGGCAATGCGCTTAACCGGGCCGATCAGCGTTATATTCCGGCTTCCACCTTTAAAATGCTGAATGCCTTGATTGGTATCCAGCATCATAAGACTTCACCAAATGAAGTATTTAAATGGGATGGACAGAAGCGGGCATTTACCAGCTGGGAAAAAGATTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCACGCCGTATTGGTCTGGAATTAATGGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCGATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGGCCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGTGGATGGGGCATGGATGTAAAACCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGTCAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCTATTGTGTATCAGGCTTTACAACAACTGGGTCTATTGCCCCAATAA", "fmax": "160763", "accession": "APSA01000003.1", "fmin": "159905", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 3623", "NCBI_taxonomy_id": "1217698", "NCBI_taxonomy_cvterm_id": "42819"}, "protein_sequence": {"accession": "ENX40034.1", "sequence": "MLFNFIVMPKKLKLLALSVVVMPSIILLGCQNIQPHVQALVTQKQTEDQIATAFENIQTSGVLVTYDGKAIQKYGNALNRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVKPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLLPQ"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-298", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38153", "model_name": "OXA-298", "model_type_id": "40292"}, "3500": {"model_id": "3500", "ARO_accession": "3001608", "model_param": {"blastp_bit_score": {"param_value": "530", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-417 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5695": {"dna_sequence": {"partial": "0", "sequence": "ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAATGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA", "fmax": "822", "accession": "KM220587.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter calcoaceticus", "NCBI_taxonomy_id": "471", "NCBI_taxonomy_cvterm_id": "39094"}, "protein_sequence": {"accession": "AIU44173.1", "sequence": "MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSNEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-417", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38008", "model_name": "OXA-417", "model_type_id": "40292"}, "3501": {"model_id": "3501", "ARO_accession": "3003115", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases. Not yet released.", "model_sequences": {"sequence": {"5696": {"dna_sequence": {"partial": "0", "sequence": "ATGTCCCGCATTCTGTTATCCAGCCTGCTTGCCGCCGGCCTCTTCTGCTCCCTGCCCGCCAGCGCCGCCACCGGCTGCATGCTGTTTGCCGATGGTAGCGGCAAGCCCTTCAGTGCCCAGGGTGACTGCGCCAGCCAGCTGCCTCCCGCCTCCACCTTCAAGATCCCGCTGGCGCTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAGCAACTGCCAGCTCTGCCATTCAAAGCCGGTGACCCTGACTTCCTGCCGGAATGGAAACAGACCACCACCCCGAGCCGTTGGATGACCTATTCGGTGATCTGGTACTCCCAACGCCTCACCGAGTGGCTGGGGGCGGCGCGCTTCCAGCAATACGTGGACCGCTTCGACTACGGCAACCGGGATCTCTCGGGCAACCCGGGCAAACATGACGGCCTGACCCAAGCCTGGCTCAGTTCCAGCCTTGCCATCAGCCCCCAGGAGCAGGCACGCTTTCTCGGCAAACTGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACGCTGCAGCACACGGCCAATATCCTGCGTCAGCCCGACATCGATGGCTGGCAGATCCATGGCAAGACCGGCACGGGCTATCCCAAACTGCTGGATGGCAGCCTCGACCGGGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAGCAGGATCAGAAGCTCATCTTCGTCCACACCGTCATCCAGAAGCCTGGCAAGCAGTTTGCCTCCCTCAGGGCCAGGGAAGAGGTGTTTGCCGCACTGCCCGAACAGCTGAAGAAACTGTGA", "fmax": "795", "accession": "KX827604.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "ARO85965.1", "sequence": "MSRILLSSLLAAGLFCSLPASAATGCMLFADGSGKPFSAQGDCASQLPPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSRWMTYSVIWYSQRLTEWLGAARFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPQEQARFLGKLVSGKLPVSAQTLQHTANILRQPDIDGWQIHGKTGTGYPKLLDGSLDRDQQIGWFVGWASKQDQKLIFVHTVIQKPGKQFASLRAREEVFAALPEQLKKL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-427", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39692", "model_name": "OXA-427", "model_type_id": "40292"}, "3502": {"model_id": "3502", "ARO_accession": "3003120", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases. Not yet released.", "model_sequences": {"sequence": {"5697": {"dna_sequence": {"partial": "0", "sequence": "ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGCATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACTATTAGGTATTTTATAG", "fmax": "845", "accession": "KM979376.1", "fmin": "20", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJG01375.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLELLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-429", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39697", "model_name": "OXA-429", "model_type_id": "40292"}, "3503": {"model_id": "3503", "ARO_accession": "3003121", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases. Not yet released.", "model_sequences": {"sequence": {"5698": {"dna_sequence": {"partial": "0", "sequence": "TTTTATAAGTCTTATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "838", "accession": "KM979377.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJG01376.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-430", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39698", "model_name": "OXA-430", "model_type_id": "40292"}, "3504": {"model_id": "3504", "ARO_accession": "3003124", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases. Not yet released.", "model_sequences": {"sequence": {"5699": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTACTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAACGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "839", "accession": "KM979378.1", "fmin": "14", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJG01377.1", "sequence": "MNIKALLLITSAIFISACSPYIVSTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-431", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39701", "model_name": "OXA-431", "model_type_id": "40292"}, "3505": {"model_id": "3505", "ARO_accession": "3003125", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases. Not yet released.", "model_sequences": {"sequence": {"5700": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAGATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "839", "accession": "KM979379.1", "fmin": "14", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJG01378.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASRSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-432", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39702", "model_name": "OXA-432", "model_type_id": "40292"}, "3506": {"model_id": "3506", "ARO_accession": "3003126", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases. Not yet released.", "model_sequences": {"sequence": {"5701": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTGATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "850", "accession": "KM979380.1", "fmin": "25", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AJG01379.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSDEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-433", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39703", "model_name": "OXA-433", "model_type_id": "40292"}, "3468": {"model_id": "3468", "ARO_accession": "3001761", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-306 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5663": {"dna_sequence": {"partial": "0", "sequence": "ATGTCAAAAAGATTAAAAACTCTCGCGTTGAGTGCATCATTTACTTTTGCTTTACCCTTGGTCGCTTGCCAGAGCTTTGGCGATCAAACACAGCACATCATGGCGCAGAAAAGTGAACAACAAAATATTGCCACCCTTTTCCAACAGGCTCAAACAAGTGGTGTATTGGTGATCTATGATGGAAAGAAAATTCAAAAATATGGCAATGACACCAGTCGCGCAGAGCAACGTTATATCCCTGCTTCAACATTTAAAATGCTGAATGCGTTAATTGGCATACAACATCATAAAACCACGCCAAATGAAGTCTTTAAATGGGATGGCCAAAAACGCGCATTCAGTAGCTGGGAAAAAGATCTCACATTAGCTGAGGCAATGCAGGCATCGGCTGTGCCTGTATATCAAGAGCTGGCACGACGGATTGGTCTGGAACTGATGACCCGTGAAGTGAAGCGAGTGGGTTATGGGAATAAGAATATTGGCACACAAGTCGATAATTTTTGGTTAGTCGGCCCATTAAAAATCACCCCTGTAGAAGAAGTACGCTTTGCCTATGCATTGGCGAAGCAAAAGCTGCCATTTGATCAATCCACTCAACAACAAGTGAAAGGCATGTTATTGATTGATGAAGTTCAAGGGACCAAGATTTACGCGAAAAGCGGCTGGGGTATGGATGTTAACCCGCAAGTGGGATGGTGGACAGGGTGGATAGAGCAAGCAAATGGCAAAGTCACGGCATTTTCATTGAATATGGAAATGAATCGGCCTGAGCATGCAGATGCCCGTAAGGCAATTGTTTATCAAGCCTTACAGCAACTGGATTTATTGGCGAATTAG", "fmax": "300792", "accession": "APSB01000022.1", "fmin": "299955", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 2100", "NCBI_taxonomy_id": "1217708", "NCBI_taxonomy_cvterm_id": "42827"}, "protein_sequence": {"accession": "ENX38336.1", "sequence": "MSKRLKTLALSASFTFALPLVACQSFGDQTQHIMAQKSEQQNIATLFQQAQTSGVLVIYDGKKIQKYGNDTSRAEQRYIPASTFKMLNALIGIQHHKTTPNEVFKWDGQKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLIDEVQGTKIYAKSGWGMDVNPQVGWWTGWIEQANGKVTAFSLNMEMNRPEHADARKAIVYQALQQLDLLAN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-306", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38161", "model_name": "OXA-306", "model_type_id": "40292"}, "3511": {"model_id": "3511", "ARO_accession": "3003597", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5706": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAATGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGCAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "JX865394.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AFZ84684.1", "sequence": "MNIKALLLITSAIFISACSPYIVSANPNHSASKSDENAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTAVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-441", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40207", "model_name": "OXA-441", "model_type_id": "40292"}, "3610": {"model_id": "3610", "ARO_accession": "3004816", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-9 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5808": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGAGTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA", "fmax": "873", "accession": "AY647246.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAT68576.1", "sequence": "MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILSLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-9", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42936", "model_name": "GOB-9", "model_type_id": "40292"}, "3611": {"model_id": "3611", "ARO_accession": "3004817", "model_param": {"blastp_bit_score": {"param_value": "590", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "HERA-2 is a class A beta-lactamase found in Atlantibacter hermannii.", "model_sequences": {"sequence": {"5809": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGACATGACGGACTTTTTACGCCAGCAAGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCACAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGATTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCGTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTGTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAAAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACGCCGGCTAACCGGGCGGTGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA", "fmax": "873", "accession": "AF398334.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Atlantibacter hermannii", "NCBI_taxonomy_id": "565", "NCBI_taxonomy_cvterm_id": "41643"}, "protein_sequence": {"accession": "AAL26995.1", "sequence": "MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRVDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRAVLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41641": {"category_aro_name": "HERA beta-lactamase", "category_aro_cvterm_id": "41641", "category_aro_accession": "3004447", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A class A beta-lactamase family shown to hydrolyze penicillin but without cephalosporinase activity."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "HERA-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42937", "model_name": "HERA-2", "model_type_id": "40292"}, "3612": {"model_id": "3612", "ARO_accession": "3004818", "model_param": {"blastp_bit_score": {"param_value": "590", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "HERA-3 is a class A beta-lactamase found in Escherichia hermannii.", "model_sequences": {"sequence": {"5810": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGACATGACGGACTTTTTACGCCAGCAAGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCACAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGATTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCGTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACGCCGGCTAACCGGGCGGTGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA", "fmax": "873", "accession": "AF398335.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Atlantibacter hermannii", "NCBI_taxonomy_id": "565", "NCBI_taxonomy_cvterm_id": "41643"}, "protein_sequence": {"accession": "AAL26996.1", "sequence": "MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRAVLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41641": {"category_aro_name": "HERA beta-lactamase", "category_aro_cvterm_id": "41641", "category_aro_accession": "3004447", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A class A beta-lactamase family shown to hydrolyze penicillin but without cephalosporinase activity."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "HERA-3", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42938", "model_name": "HERA-3", "model_type_id": "40292"}, "3590": {"model_id": "3590", "ARO_accession": "3004793", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FONA-6 is a class A beta-lactamase gene found in Serratia fonticola.", "model_sequences": {"sequence": {"5788": {"dna_sequence": {"partial": "0", "sequence": "ATGGTTAAAAATACATTACGTCAAACCACCCTGATGGTGGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAGCTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGCGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATTGGCGATAAAACCTTCCGCCTCGATCGTACCGAACCCACTTTAAATACCGCCATTCCAGGTGATAAGCGTGATACCACCTCACCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCAAGCATTCGCGCAGGTCTGCCAACTACATGGGTGGTTGGGGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTAATTTGGCCAGCGAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCTCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTTACCGAAGGGCTTTGA", "fmax": "1941", "accession": "AJ251244.1", "fmin": "1053", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Serratia fonticola", "NCBI_taxonomy_id": "47917", "NCBI_taxonomy_cvterm_id": "39675"}, "protein_sequence": {"accession": "CAB61645.1", "sequence": "MVKNTLRQTTLMVATVMPLLFGSAPLWAQTANAKANIQQQLSELEKSSGGRLGVALIDTADNSQILYRADERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42905": {"category_aro_name": "FONA beta-lactamase", "category_aro_cvterm_id": "42905", "category_aro_accession": "3004787", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FONA is a class A beta-lactamase gene family found in Serratia fonticola."}}, "ARO_name": "FONA-6", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42911", "model_name": "FONA-6", "model_type_id": "40292"}, "3597": {"model_id": "3597", "ARO_accession": "3004803", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-11 is a class B beta-lactamase gene found in Chryseobacterium meningosepticum.", "model_sequences": {"sequence": {"5795": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGCTACACTGTTTTTTTTATCAGCTTGTTTGAGTTTAAGTTTGAATGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGGAACCTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTTATTAATACAGGAACAGCAGAATCGCTTACAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGGTCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTAGAGGATTTTAAAACAGAAACCGGTGCAAAATTCTATGCAGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGGAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTGCAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGACCTTTGGGTGGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCATACAATCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAA", "fmax": "879", "accession": "AY647248.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAT68578.1", "sequence": "MRNFATLFFLSACLSLSLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLTIIKGNIQKLGFNYKDIKVLLLTQAHYDHTGALEDFKTETGAKFYADKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVAAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-11", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42923", "model_name": "GOB-11", "model_type_id": "40292"}, "3596": {"model_id": "3596", "ARO_accession": "3004802", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-10 is a class B beta-lactamase gene found in Chryseobacterium meningosepticum.", "model_sequences": {"sequence": {"5794": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAA", "fmax": "873", "accession": "AY647247.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAT68577.1", "sequence": "MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-10", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42922", "model_name": "GOB-10", "model_type_id": "40292"}, "3595": {"model_id": "3595", "ARO_accession": "3004801", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FTU-1 is a class A beta-lactamase gene found in Francisella tularensis. It causes Tularemia.", "model_sequences": {"sequence": {"5793": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTCTATTAGTTACAACTTTATCATTAATCCCGAGTATCATACTAGCTGCTCCTCAATTAGATGATTCTTTTAAAAATCTGGAAAACAAATATGATGGAAAAATTGGCATCTACACTCTCAACACTGATGATAAAACTAACATCAAATATAACGAAAGCTATCACTTCCCTATTTGTAGTGTTTTCAAGTTTTTATTAGTTGGTGCAATTTTAGATTATGATATGCATAATCAAGGCTTCTTAGATAAAAAAATTCCAATAAATCAAGATGATATTGGTAAACTCGGATATGCTCCTATTACTGCTAAAAACGTTGGTAAAACTCTAACAATATCACAACTTAACTACGCTGCTATCCTAAGTGATAGTCCTGCCAGTAACATATTAGTTAGAGAACTTGGAGGTTTACAAAACTTAAATAAATTTATAAAAAAATTAGGTGATAACGATACTATAATTACTGCTGATGAACCAGAAATTAATTATACTCAGCCACATAGTAATATAAATAAAACAACTCCAAAGGCTATTACTAAAGATATTTATAAATTAGCATTTGGCAATATTCTAGATAAAAAACATAAAGATATTTTTATAAAGTATCTACAAGATAATAATACTGGTGCAAATAGAATAGCTTTTAGCATGCCTAAAGATTGGATAATTGGCGATAAAACTGGAACTTGTGGTCAATATGCAGCAACTAATGATGTAGCTATTATATGGCCTAAAAATCAGCAACCTATTGCGTTAGGAATTTTATATACTAACCCTAATGATAAAAATGCACCAAGTAATGAAGAAATTATTCAACAAGCAGCTAAATTAATAGCTAATGATCTGACTAACACTTATAAATAA", "fmax": "631167", "accession": "CP001633.1", "fmin": "630303", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Francisella tularensis subsp. tularensis NE061598", "NCBI_taxonomy_id": "510831", "NCBI_taxonomy_cvterm_id": "42921"}, "protein_sequence": {"accession": "ADA78299.1", "sequence": "MRLLVTTLSLIPSIILAAPQLDDSFKNLENKYDGKIGIYTLNTDDKTNIKYNESYHFPICSVFKFLLVGAILDYDMHNQGFLDKKIPINQDDIGKLGYAPITAKNVGKTLTISQLNYAAILSDSPASNILVRELGGLQNLNKFIKKLGDNDTIITADEPEINYTQPHSNINKTTPKAITKDIYKLAFGNILDKKHKDIFIKYLQDNNTGANRIAFSMPKDWIIGDKTGTCGQYAATNDVAIIWPKNQQPIALGILYTNPNDKNAPSNEEIIQQAAKLIANDLTNTYK"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42919": {"category_aro_name": "FTU beta-lactamase", "category_aro_cvterm_id": "42919", "category_aro_accession": "3004800", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FTU is a class A beta-lactamase gene family found in Francisella tularensis."}}, "ARO_name": "FTU-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42920", "model_name": "FTU-1", "model_type_id": "40292"}, "3594": {"model_id": "3594", "ARO_accession": "3004799", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "FRI-3 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter cloacae.", "model_sequences": {"sequence": {"5792": {"dna_sequence": {"partial": "0", "sequence": "ATGTTTTTTTTAAAAAAAGCGCAAGTACATTTATTTTTTTTTCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATAGTATTGAGCAAATGAGGGAATTGGAAGCTGCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAGAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCATTCCTCGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGCAAAACAGGAGCAAGCGTGCGGACTTTGGCGAAGGCAGCAATTCAGTACAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGATGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGCCAGACGCTAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAAATTCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTTATAAATAA", "fmax": "885", "accession": "KY524440.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "AQS23610.1", "sequence": "MFFLKKAQVHLFFFLCLPLNSFASQESNSIEQMRELEAAFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKKTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRKTGASVRTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWDVGDKTGTCGFYGTANDVAILWPDANSPAVMAVYTTRPNQNDKHDEAVIKNSAKIAINAVYGSYK"}}}}, "ARO_category": {"42915": {"category_aro_name": "FRI beta-lactamase", "category_aro_cvterm_id": "42915", "category_aro_accession": "3004796", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "FRI-3", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42918", "model_name": "FRI-3", "model_type_id": "40292"}, "3599": {"model_id": "3599", "ARO_accession": "3004805", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-13 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5797": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAATTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTACAGGATTTCAAAACAGAAACCGGTGCAAAATTCTATACCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGACACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGTCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCCCAAGATAAATAA", "fmax": "879", "accession": "AY647250.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAT68580.1", "sequence": "MRNFATLFFLSVCLNLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYTDKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFDTKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-13", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42925", "model_name": "GOB-13", "model_type_id": "40292"}, "3598": {"model_id": "3598", "ARO_accession": "3004804", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-12 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5796": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGCTACACTGTTTTTCATGTTCGTTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCATTCAGAATTGCAGGGAACCTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCTATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGGGATCCGTACAATCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAA", "fmax": "873", "accession": "AY647249.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAT68579.1", "sequence": "MRNFATLFFMFVCLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGKSDYEMGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-12", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42924", "model_name": "GOB-12", "model_type_id": "40292"}, "3510": {"model_id": "3510", "ARO_accession": "3003596", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5705": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATAAAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA", "fmax": "822", "accession": "KP727574.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AKR53962.1", "sequence": "MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDKKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-440", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40206", "model_name": "OXA-440", "model_type_id": "40292"}, "3452": {"model_id": "3452", "ARO_accession": "3001743", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-288 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5648": {"dna_sequence": {"partial": "0", "sequence": "ATGATGATGTCGAAAAAATTAAAATGTCTGGCCTTTTTTACAGCCATCTTTTTTGCAATTCCCATGACTGCTTGTCAAAGTTTTAGCCAACAAAAGCAACAGCTCTCGACACAAAAAAATGAGCAGCAGCAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAGTGGTGTTTTGGTGATTTATGATGGTAAGAAAATTCAAAGCTATGGCAATGATCTTGATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGTTAAACGCCTTGATCGGAATACAGCATCATAAGACCACACCAGATGAAATGTTTAAATGGGATGGCAAAAAGCGAGCATTTAGCAGTTGGGAAAAAGATTTAACCTTAGCTGAGGCGATGCAGGCATCGGCGGTACCTGTCTATCAAGAATTGGCAAGACGTATTGGTCTGGAACTGATGACTCGGGAAGTTAAGCGAGTGGGCTATGGCAATAAAAATATAGGAACTCAAGTCGATAACTTTTGGTTAGTAGGCCCATTAAAAATTACGCCTGTAGAGGAAGTACGCTTTGCCTACGCATTAGCGAAGCAGAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTAAAAGGCATGTTATTGATTGATGAGGTTCAAGGCACCAAGATCTACGCTAAAAGTGGTTGGGGGATGGACGTTAGCCCACAAGTGGGATGGTGGACAGGTTGGATAGAGCAAGCAAATGGCAAGATCACCGCATTTTCATTAAATATGGAAATGAGTCGACCAGAGCATGCGGAGGCACGGAAGGCGATTGTTTATCAAGCTTTGCAGCAGCTAGATTTATTGGCGAATTAG", "fmax": "307932", "accession": "APRN01000033.1", "fmin": "307089", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. CIP 70.18", "NCBI_taxonomy_id": "1217700", "NCBI_taxonomy_cvterm_id": "42813"}, "protein_sequence": {"accession": "ENX60508.1", "sequence": "MMMSKKLKCLAFFTAIFFAIPMTACQSFSQQKQQLSTQKNEQQQISSLFQSAQTSGVLVIYDGKKIQSYGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEMFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLIDEVQGTKIYAKSGWGMDVSPQVGWWTGWIEQANGKITAFSLNMEMSRPEHAEARKAIVYQALQQLDLLAN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-288", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38143", "model_name": "OXA-288", "model_type_id": "40292"}, "3450": {"model_id": "3450", "ARO_accession": "3001740", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-285 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5646": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAATTCTGATTTTGCTACCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTACCTCACCTGTTTCATCTTTCCCTTCTCAGATCACTTCAACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGTTCTGGCGTTTTAGTGATTCAGCGTGGTCAAAAAGTACAGGTCTATGGCAATGATTTAAGCCGTGCAGGTACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGTCTACAACATGGTAAAGCCACAACCAATGAGATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACGCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCATATTGGTTTGGAATTAATGCAGCAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTCTCTGCTCTAGCCCGAGAGCAACTAGCCTTTGATCCTCAAGTCCAGCAGCAAGTTAAAGCCATGTTACTTTTACAGGAACGGCAAGCTTATCGCCTATATGCCAAATCCGGTTGGGGCATGGATGTACAACCTCAAGTCGGCTGGCTTACCGGCTGGGTTGAAACACCGCAAGCCGAGATCGTGTCATTTTCACTGAATATGCAGATGCAAAATGGTATGGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA", "fmax": "65827", "accession": "APRY01000059.1", "fmin": "64996", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. CIP 64.7", "NCBI_taxonomy_id": "1144673", "NCBI_taxonomy_cvterm_id": "42811"}, "protein_sequence": {"accession": "ENX26326.1", "sequence": "MKILILLPLLSCLGLTACTSPVSSFPSQITSTQSTQAIAQLFDQAQSSGVLVIQRGQKVQVYGNDLSRAGTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARHIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLLLQERQAYRLYAKSGWGMDVQPQVGWLTGWVETPQAEIVSFSLNMQMQNGMDPAIRLEILQQALAELGLYPKAEG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-285", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38140", "model_name": "OXA-285", "model_type_id": "40292"}, "3451": {"model_id": "3451", "ARO_accession": "3001742", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-287 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5647": {"dna_sequence": {"partial": "0", "sequence": "ATGTCGAAAAAATTAAAATGTCTGGCCCTTTTTACCGCTGTCTTTTTTGCAATTCCCATGACTGCTTGTCAAAGTTTTAGCCAACAAAAGCAACAGTTCTCGACACAAAAAAATGAGCAGCAACAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAGTGGTGTTTTGATGATTTATGATGGCAAGAAAATTCAAAGCTATGGCAATGATCTTGATCGTGCAGAACAGCGCTATATCCCTGCTTCAACCTTTAAAATGTTAAACGCCTTGATCGGAATACAGCATCATAAGACCACACCAGATGAAGTATTTAAATGGGATGGCAAAAAGCGGGCATTTAGTAGTTGGGAAAAAGATTTAACCTTAGCTGAGGCGATGCAGGCATCAGCGGTACCTGTCTATCAAGAATTGGCAAGACGTATTGGTTTGGAACTGATGACCCGTGAAGTAAAGCGCGTGGGTTATGGTAATAAAAATATCGGGACACAAGTCGATAATTTCTGGTTAGTTGGCCCCTTAAAAATCACTCCCATAGAAGAAGTTCGTTTTGCCTATGCGCTGGCAAAACAGAAATTGCCATTTGACCAGCCGACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACCAAAATCTATGCCAAAAGTGGTTGGGGTATGGATGTCAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGCAAGATCACTGCCTTCTCACTGAATATGCAAATGAGTCAGCCTGAACATGCAGATGCACGTAAAGTGATTGTGTATCAAGCCTTGCAAGAGTTGGGATTGTTAGCCCATTAA", "fmax": "937", "accession": "NG_050609.1", "fmin": "100", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. CIP 56.2", "NCBI_taxonomy_id": "1144672", "NCBI_taxonomy_cvterm_id": "42812"}, "protein_sequence": {"accession": "WP_032865068.1", "sequence": "MSKKLKCLALFTAVFFAIPMTACQSFSQQKQQFSTQKNEQQQISSLFQSAQTSGVLMIYDGKKIQSYGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPIEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKVIVYQALQELGLLAH"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-287", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38142", "model_name": "OXA-287", "model_type_id": "40292"}, "3456": {"model_id": "3456", "ARO_accession": "3001748", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-293 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5651": {"dna_sequence": {"partial": "0", "sequence": "ATGTCGGCGAAACTAAAAATTCTCACTTTATCCATTTCATTGGTGCTGGGATTACCCTTGATGGCTTGCCAGAGCTTTAGTCAACAAAAGCAGCAAATAATGACACAGAAAAGTGAACAGCAGCAGATTGCGAGCTTATTCCAAAATGCTCAAACTAGCGGTGTTTTGGTCATTTATGATGGAAAGAAAATTCAAAAATATGGCAATGACACCAGTCGCGCAGAGCATCGTTATATCCCAGCCTCAACTTTTAAAATGCTGAATGCGTTAATTGGCATACAGCATCATAAAACCACGCCAAATGAAATCTTTAAATGGGATGGACGGAAACGCGCATTCAGTAGTTGGGAAAAAGACCTCACACTAGCGGAGGCGATGCAGGCATCAGCTGTGCCTGTGTATCAAGAGCTGGCACGACGTATTGGCCTAGAACTGATGACCCAAGAAATTAAGCGAGTGGGTTATGGCAATAACAATGTTGGGACACAGGTCGATAATTTCTGGTTAGTTGGCCCATTAAAAATTACTCCTGTGGAAGAAGTACGCTTTGCCTACGCATTGGCGAAGCAAAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTGAAAGGCATGTTATTGCTTGATGAAGTTCAGGGGGCCAAGATATACGCTAAAAGTGGTTGGGGTATGGATGTTAGTCCGCAAGTTGGATGGTGGACGGGTTGGATAGAACAAGCAAATGGCAAGATCACCGCATTTTCATTAAATATGGAAATGAGTCAACCTGAGCATGCAGAGACACGTAAGGCGATTGTTTATCAAGCTTTGCAGCAACTTGATTTATTGGTGAATTAG", "fmax": "937", "accession": "NG_050610.1", "fmin": "100", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. ANC 3929", "NCBI_taxonomy_id": "1217707", "NCBI_taxonomy_cvterm_id": "42816"}, "protein_sequence": {"accession": "WP_032877719.1", "sequence": "MSAKLKILTLSISLVLGLPLMACQSFSQQKQQIMTQKSEQQQIASLFQNAQTSGVLVIYDGKKIQKYGNDTSRAEHRYIPASTFKMLNALIGIQHHKTTPNEIFKWDGRKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTQEIKRVGYGNNNVGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLLDEVQGAKIYAKSGWGMDVSPQVGWWTGWIEQANGKITAFSLNMEMSQPEHAETRKAIVYQALQQLDLLVN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-293", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38148", "model_name": "OXA-293", "model_type_id": "40292"}, "3457": {"model_id": "3457", "ARO_accession": "3001749", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-294 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5652": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAATTAAAATTACTCGCGCTATGTGCAACTGTAATCTCAGCTGCAACACTGGTCGGTTGTCAAAATATTCAGTCCCAAGCTCAACCTCTAGTCTTAAAGAAACAGGCTCAGGATCAGATTGCAACTGCATTCGAAAATATCCAGACAACTGGTGTATTGGTCACCTATGACGGCAAAAATTTTCAAAGATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCTGCTTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCACCATAAAACCTCACCCAATGAAGTGTTTAAATGGGATGGACAGAAACGGGCTTTTCGTAGCTGGGAGCAGGACTTAACGCTTGCTGAGGCAATGCAGGCTTCGGCTGTACCTGTCTATCAGGAGCTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGCTACGGCAATCAAAATATAGGGACACAATTTGATAATTTCTGGTTGGTGGGGCCTTTAGAAATTACGCCAGTTGAGGAAGTGAAATTTGCTTATGCCTTAGCCAAACAGCAACTTCCATTTGCTCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACCAGAATCTATGCCAAAAGTGGTTGGGGAATGGATGTAAATCCTCAAGTCGGATGGTGGACAGGTTGGGTTGAACAACCAAATGGTCAAATCACTGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCGGATGCGCGTAAAGCCATTGTTTATCAAGCTTTACAACAGTTAGGTTTATTACCTCAATAA", "fmax": "270698", "accession": "APPC01000015.1", "fmin": "269861", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 758", "NCBI_taxonomy_id": "1217712", "NCBI_taxonomy_cvterm_id": "41199"}, "protein_sequence": {"accession": "ENU93232.1", "sequence": "MSKKLKLLALCATVISAATLVGCQNIQSQAQPLVLKKQAQDQIATAFENIQTTGVLVTYDGKNFQRYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEQDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGTQFDNFWLVGPLEITPVEEVKFAYALAKQQLPFAPSTQQQVRDMLLIENVQGTRIYAKSGWGMDVNPQVGWWTGWVEQPNGQITAFSLNMEMKKAEHADARKAIVYQALQQLGLLPQ"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-294", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38149", "model_name": "OXA-294", "model_type_id": "40292"}, "3454": {"model_id": "3454", "ARO_accession": "3001746", "model_param": {"blastp_bit_score": {"param_value": "530", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-291 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5649": {"dna_sequence": {"partial": "0", "sequence": "ATGTCAAAAAAACTAAAAATGCTCACTTTATCTATTTCAATGATGCTGGGCTTACCCTTGATGGCTTGCCAGAGCTTTAGTCAACAAAAGCAGCAAATAATGACACAGGAACGTGAACAACAGCAGATTACGAGTTTATTCCAAAATGCTCAAACCAGCGGTGTTTTGGTTATTTATGATGGAAAGAAAATTCAAAAATTTGGCAATGACGTACATCGTGCAGATCAGCGCTATATCCCAGCCTCGACCTTTAAAATGCTGAATGCGTTAATTGGTATACAGCATCATAAAACTACGCCAAAAGAAGTCTTTAAATGGGATGGACAGAAACGCGCATTCAGTAGTTGGGAAAAAGATCTCACATTAGCTGAGGCAATGCAGGCATCGGCTGTGCCTGTGTATCAAGAGCTGGCACGACGTATTGGTCTGGAGCTGATGACTCGTGAAGTTAAGCGAGTGGGCTATGGAAATAAGAATATTGGGACACAAGTCGATAACTTTTGGTTGGTTGGTCCATTAAAAATTACGCCTGTGGAGGAAGTACGTTTTGCCTACGCATTGGCGAAGCAAAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTAAAAGGCATGTTATTGGTGGATGAGGTTCATGGCACCAAAATATACGCCAAAAGTGGCTGGGGTATGGATGTTAGCCCGCAAGTGGGATGGTGGACAGGTTGGATAGAGCAAGCAAATGGCAAGATCACCGCATTTTCATTAAATATGGAAATGAGTCGACCTGAGCATACTGAGGCACGGAAGGCGATTGTTTATCAAGCTTTGCAGCAGCTAGATTTATTGGCGAATTAG", "fmax": "280280", "accession": "APRL01000010.1", "fmin": "279443", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. ANC 4105", "NCBI_taxonomy_id": "1217703", "NCBI_taxonomy_cvterm_id": "42814"}, "protein_sequence": {"accession": "ENW94121.1", "sequence": "MSKKLKMLTLSISMMLGLPLMACQSFSQQKQQIMTQEREQQQITSLFQNAQTSGVLVIYDGKKIQKFGNDVHRADQRYIPASTFKMLNALIGIQHHKTTPKEVFKWDGQKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLVDEVHGTKIYAKSGWGMDVSPQVGWWTGWIEQANGKITAFSLNMEMSRPEHTEARKAIVYQALQQLDLLAN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-291", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38146", "model_name": "OXA-291", "model_type_id": "40292"}, "3455": {"model_id": "3455", "ARO_accession": "3001747", "model_param": {"blastp_bit_score": {"param_value": "530", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-292 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5650": {"dna_sequence": {"partial": "0", "sequence": "ATGTCGAAAAAACTAAAAATGCTCACTTTATCTATTTCAATGATGCTGGGCTTACCCTTGATGGCTTGCCAGAGCTTTAGTCAACAAAAGCAGCAAATAATGACACAGGAAAGTGAACAACAGCAGATTGCGAGTTTATTCCAAAATGCTCAAACCAGCGGTGTTTTGGTCATTTATGATGGAAAGAAAATTCAAAAATTTGGCAATGATGTACATCGTGCAGATCAGCGCTATATCCCAGCTTCGACCTTTAAAATGCTGAATGCGTTAATTGGCATACAGCATCATAAAACTACGCCAAAAGAAGTCTTTAAATGGGATGGACAGAAACGCGCATTCAGTAGTTGGGAAAAAGATCTCACATTAGCTGAGGCAATGCAGGCATCGGCTGTGCCTGTGTATCAAGAGCTGGCACGACGTATTGGTCTGGAACTGATGACTCGGGAAGTGAAGCGAGTGGGCTATGGCAATAAGAATATAGGGACACAAGTCGATAATTTTTGGTTAGTAGGCCCATTAAAAATTACGCCTGTAGAGGAAGTACGCTTTGCCTACGCATTGGCGAAGCAAAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTAAAAGGCATGTTATTGATTGATGAGGTTCAAGGCACCAAGATCTACGCTAAAAGTGGTTGGGGTATGGATGTTAGCCCGCAAGTGGGATGGTGGACAGGTTGGATAGAGCAAGCAAATGGCAAGGTCACCGCATTTTCATTAAATATGGAAATGAGTCGACCTGAGCATGCGGAGGCACGGAAGGCGATTGTTTATCAAGCTTTGCAGCAACTGGATTTATTGGCGAATTAG", "fmax": "300775", "accession": "APRO01000007.1", "fmin": "299938", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 1867", "NCBI_taxonomy_id": "1217702", "NCBI_taxonomy_cvterm_id": "42815"}, "protein_sequence": {"accession": "ENX53612.1", "sequence": "MSKKLKMLTLSISMMLGLPLMACQSFSQQKQQIMTQESEQQQIASLFQNAQTSGVLVIYDGKKIQKFGNDVHRADQRYIPASTFKMLNALIGIQHHKTTPKEVFKWDGQKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLIDEVQGTKIYAKSGWGMDVSPQVGWWTGWIEQANGKVTAFSLNMEMSRPEHAEARKAIVYQALQQLDLLAN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-292", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38147", "model_name": "OXA-292", "model_type_id": "40292"}, "3513": {"model_id": "3513", "ARO_accession": "3003599", "model_param": {"blastp_bit_score": {"param_value": "545", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5708": {"dna_sequence": {"partial": "0", "sequence": "ATGACGAAACTCCGCCACGCCACCACCGGCGCCTTCCTTGCCGCCCTGGCCACCTTCGCCCATGCCGAACACCCTGTCTGCACGCTCGTTGCCGACGCCGCCACGGGCAAGGTCGTCCTGCAGGAGGGCAAGTGCAACGAGCGCGTGACGCCGGCGTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGCTACGACGCCGGCTTCCTGAAAGACCCGCACACGCCGGTCGAACACTTCAGGCGCGGCGACCCCGACTGGGGCGGCCGGCCGTGGCGCCAGCCTGTCGACCCGACGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCCCAGCGCATCACCCACGCGATGGGCGCGCAGATGTTCGCCTCGTACGTGCGCAAGCTCGACTACGGCAACATGGATGTGAGCGGCGACCCGGGCAAGAACAACGGCCTGGATCGCTCGTGGATCACCTCGTCGCTGAAGATCTCGCCCGAGGAGCAGGTCGGCTTTCTGCGCCGGCTCGTCAACCGGCAGTTGCCCGTGTCGGCGCAGACGTACGAGATGGTCGACCGCACCGTGCAGACGTGGCAGGTGCCCGGCGGCTGGGCCGTGCAGGGCAAGACGGGCACGGCGGGCCCGGCGCCGGGCAATACCTCGGCCGACGGCACGTGGGATCAGGCCCACGCTTATGGCTGGTTTGTCGGCTGGGCGAAGAAAGGAGGCCGGACCTACGTGTTTGCGAACCTGATCCAGGACGACAAGATCGAGCCCACCTCGGGCGGCATCCGCTCGCGCGACGCGATGCTGGCGCGCCTGCCGCAGGTGCTGGCTGCCGCCAAGCCCTGA", "fmax": "670683", "accession": "CM009147.1", "fmin": "669855", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Ralstonia mannitolilytica", "NCBI_taxonomy_id": "105219", "NCBI_taxonomy_cvterm_id": "42837"}, "protein_sequence": {"accession": "PLT17746.1", "sequence": "MTKLRHATTGAFLAALATFAHAEHPVCTLVADAATGKVVLQEGKCNERVTPASTFKLALAVMGYDAGFLKDPHTPVEHFRRGDPDWGGRPWRQPVDPTLWLKYSVVWYSQRITHAMGAQMFASYVRKLDYGNMDVSGDPGKNNGLDRSWITSSLKISPEEQVGFLRRLVNRQLPVSAQTYEMVDRTVQTWQVPGGWAVQGKTGTAGPAPGNTSADGTWDQAHAYGWFVGWAKKGGRTYVFANLIQDDKIEPTSGGIRSRDAMLARLPQVLAAAKP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-443", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40209", "model_name": "OXA-443", "model_type_id": "40292"}, "3512": {"model_id": "3512", "ARO_accession": "3003598", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5707": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGTAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KP844571.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AKU37610.1", "sequence": "MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLVMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-442", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40208", "model_name": "OXA-442", "model_type_id": "40292"}, "3458": {"model_id": "3458", "ARO_accession": "3001750", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-295 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5653": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAATTAAAATTACTCGCGCTATGTGCAACTGTAATCTCAGCTGCAACACTGGTCGGTTGTCAAAATATTCAGTCCCAAGCTCAACCTCTAGTCTTAAAGAAACAGACGCAGGATCAGATCGCAACTGCATTCGAAAATATCCAGACAACTGGTGTATTAGTCACCTATGATGGCAAAAATTTTCAAAAATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCGGCCTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCACCATAAAACCTCACCTAATGAAGTGTTTAAATGGGATGGACAGAAACGGGCTTTCCGTAGCTGGGAGAAGGACTTAACGCTTGCTGAGGGAATGCAGGCTTCGGCTGTACCTGTCTATCAGGAGCTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGCTACGGTAATCAAAATATAGGGGCGCAAGTTGATAATTTTTGGTTAGTGGGGCCTTTGGAGATTACGCCAGTTGAGGAAGTAAAATTTGCTTATGCCTTAGCCAAACAGCAACTTCCATTTGATCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACCAGAATCTATGCCAAGAGTGGTTGGGGAATGGATGTAAATCCTCAAGTTGGATGGTGGACGGGTTGGATTGAACAAACGAATGGTCAAATCACAGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCGGATGCGCGTAAAGCGATTGTTTATCAAGCTTTACAACAGTTAGGTTTATTACCTCAATAA", "fmax": "274795", "accession": "APRW01000016.1", "fmin": "273958", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 2168", "NCBI_taxonomy_id": "1217706", "NCBI_taxonomy_cvterm_id": "42817"}, "protein_sequence": {"accession": "ENX19403.1", "sequence": "MSKKLKLLALCATVISAATLVGCQNIQSQAQPLVLKKQTQDQIATAFENIQTTGVLVTYDGKNFQKYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEKDLTLAEGMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGAQVDNFWLVGPLEITPVEEVKFAYALAKQQLPFDPSTQQQVRDMLLIENVQGTRIYAKSGWGMDVNPQVGWWTGWIEQTNGQITAFSLNMEMKKAEHADARKAIVYQALQQLGLLPQ"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-295", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38150", "model_name": "OXA-295", "model_type_id": "40292"}, "3459": {"model_id": "3459", "ARO_accession": "3001752", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-297 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5654": {"dna_sequence": {"partial": "0", "sequence": "GTGTTGTTCAATTTTATAGTCATGCCGAAAAAATTAAAATTACTCGTTCTATCTGTAGTTGTGATGCCCTCAATAATATTGTTGGGCTGCCAAAATATTCAGCCACACGTTCAAACTTTAGTCACGCAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTCACCTATGATGGCAAAGCTATTCAAAAATATGGCAATGCGCTTAACCGGGCCAATCAGCGCTATATTCCGGCTTCCACCTTTAAAATGCTGAATGCCTTGATTGGTATCCAGCATCACAAGACTTCACCGAATGAAGTATTTAAATGGGATGGACAGAAGCGGGTATTTACCAGCTGGGAAAAAGATTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCACGCCGTATCGGTCTGGAATTAATGGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCAATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGGCCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGTGGATGGGGCATGGATGTAAAACCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGTCAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCTATTGTGTATCAGGCTTTACAACAACTGGGTCTATTGCCCCAATAA", "fmax": "288976", "accession": "APRR01000006.1", "fmin": "288118", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 1847", "NCBI_taxonomy_id": "1217697", "NCBI_taxonomy_cvterm_id": "42818"}, "protein_sequence": {"accession": "ENX09209.1", "sequence": "MLFNFIVMPKKLKLLVLSVVVMPSIILLGCQNIQPHVQTLVTQKQTEDQIATAFENIQTSGVLVTYDGKAIQKYGNALNRANQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRVFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVKPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLLPQ"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-297", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38152", "model_name": "OXA-297", "model_type_id": "40292"}, "3517": {"model_id": "3517", "ARO_accession": "3003604", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5712": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCATCTTGTTTTTATGGATTTTAAATTTTGCCTTTGGACAAGATAAAATATTAGAAGATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAATCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCAAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACTTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCCTTTTCCAATAAAAGTCAAGAAGAAGTTAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAATTAA", "fmax": "747", "accession": "KR061497.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29909.1", "sequence": "MKKIILFLWILNFAFGQDKILEDFFKDYNTSGTFIIFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSNKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKDIKNIKIREELLEKYIYSLN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-448", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40214", "model_name": "OXA-448", "model_type_id": "40292"}, "3516": {"model_id": "3516", "ARO_accession": "3003603", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5711": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCTATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAATTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTTCAACAATAATAGGATTAAAAGCTTTTACTGA", "fmax": "774", "accession": "KR061496.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29908.1", "sequence": "MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFKRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKIQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFFNNNRIKSFY"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-447", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40213", "model_name": "OXA-447", "model_type_id": "40292"}, "3515": {"model_id": "3515", "ARO_accession": "3003602", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5710": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTCTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATATTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA", "fmax": "750", "accession": "KR061495.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29907.1", "sequence": "MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFQRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNIDIKDIKNIKIREELLEKYLAIITN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-446", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40212", "model_name": "OXA-446", "model_type_id": "40292"}, "3514": {"model_id": "3514", "ARO_accession": "3003600", "model_param": {"blastp_bit_score": {"param_value": "525", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5709": {"dna_sequence": {"partial": "0", "sequence": "ATGTTCTCTCGTTGGTCGAAACCTCTCGTGCTTGCCGCCACGGTGTGCGCCATGGCGATGAGCGCCGCCACCGCCCACGCCGAACTCATCGTGCGCAACGATCTCAAGCGCGTGTTCGACGAGGCCGGCGTCTCCGGTACCTTCGTCCTGATGGATATCAGCGCCGACCGCACCTACGTCGTTGACCCGGCCCGCGCCGCGCGGCGCATTCATCCGGCCTCAACTTTCAAGATCCCGAACAGCCTCATCGCCTTCGACACGGGCGCGGTGCGTGACGATCATGAAGTGCTGCCATACGGCGGCAAGCCGCAGCCCTACAAGCAGTGGGAGCACGACATGGCGCTGCCCGAGGCGATCCGCCTGTCGGCCGTGCCGATCTACCAGGAAGTGGCGCGCCGCGTCGGCTTGGAGCGCATGCAGGCGTATGTCGATGCGTTCGACTATGGCAATCGCCAGCTTGGCAGCGTGATCGACCAGTTCTGGCTGCGCGGTCCGCTCGAAATCTCGGCGCTTGAAGAGGCGCGCTTCACCAGCCGCATGGCGCTCAAGCAGTTGCCGGTGAAGCCGCGCACGTGGGACATGGTTCACCGCATGCTGCTGATCGAGCAGCAAGGGGATGCCGCGCTGTACGCCAAGACCGGCGTCGCCACGGAATACCAGCCGGAGATCGGCTGGTGGGTCGGCTGGGTCGAGCGTGCCGGACGCGTCTATGCCTTTGCGCTGAACATCGACATGCCGCGCGAGGGCGACATGGCCAAGCGCATTCCGCTGGGCAAGCAGTTGATGCAGGCGCTGGACGTGTGGCCGGTACTCTGA", "fmax": "816", "accession": "LC030179.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Ralstonia mannitolilytica", "NCBI_taxonomy_id": "105219", "NCBI_taxonomy_cvterm_id": "42837"}, "protein_sequence": {"accession": "BAQ55594.1", "sequence": "MFSRWSKPLVLAATVCAMAMSAATAHAELIVRNDLKRVFDEAGVSGTFVLMDISADRTYVVDPARAARRIHPASTFKIPNSLIAFDTGAVRDDHEVLPYGGKPQPYKQWEHDMALPEAIRLSAVPIYQEVARRVGLERMQAYVDAFDYGNRQLGSVIDQFWLRGPLEISALEEARFTSRMALKQLPVKPRTWDMVHRMLLIEQQGDAALYAKTGVATEYQPEIGWWVGWVERAGRVYAFALNIDMPREGDMAKRIPLGKQLMQALDVWPVL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-444", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40210", "model_name": "OXA-444", "model_type_id": "40292"}, "3603": {"model_id": "3603", "ARO_accession": "3004809", "model_param": {"blastp_bit_score": {"param_value": "519", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-2 is class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5801": {"dna_sequence": {"partial": "1", "sequence": "AAAGAACCTGAAAATATGCCCAATGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACCTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT", "fmax": "756", "accession": "AF189296.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAF89152.1", "sequence": "KEPENMPNEWNQAYEPFRIAGNLYYLGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42929", "model_name": "GOB-2", "model_type_id": "40292"}, "3467": {"model_id": "3467", "ARO_accession": "3001760", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-305 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5662": {"dna_sequence": {"partial": "0", "sequence": "ATGTATAAAAAAGTCCTTGTCGTTGCAACAGCTACTCTATTTTTATCTGCCTGCTCTTCTAACACGGTAAAACAACATCAAATACATTCTATTTCCGCCAATAAAAATTCAGAAGAAATTAAATCTCTGTTTGATCAGGCACAGACCACAGGAGTTTTAGTGGTTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAACTGAAATATTTAAATGGGATGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCTCGTCGTATTAGACTTGATCTTATGACTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTTAAAATTACACCTGAGCAAGAAACCCAATTTGCTTATAAATTAGCTAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAGCAAGTCCAATCAATGGTGTTTATAGAAGAAAAAAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGCTGGTTAACCGGCTGGGTCGTTCAACCGCAAGGAGAAATTGTGGCATTCTCGCTCAATTTAGAAATGAAAAAAGGAATCCCTAGTTCTATCCGAAAAGAGATTGCTTATAAGGGATTAGAACAACTCGGCGTTTTATAA", "fmax": "349654", "accession": "APPF01000021.1", "fmin": "348832", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 817", "NCBI_taxonomy_id": "520708", "NCBI_taxonomy_cvterm_id": "42826"}, "protein_sequence": {"accession": "ENV02983.1", "sequence": "MYKKVLVVATATLFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVVKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIRLDLMTKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-305", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38160", "model_name": "OXA-305", "model_type_id": "40292"}, "3601": {"model_id": "3601", "ARO_accession": "3004807", "model_param": {"blastp_bit_score": {"param_value": "555", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-15 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5799": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAATTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAACCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTACAGGATTTCAAAACAGAAACCGGTGCAAAATTCTATACCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGACACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGTCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCCCAAGATAAATAA", "fmax": "879", "accession": "AY775547.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAV65595.1", "sequence": "MRNFATLFFLSVCLNLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAEPLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYTDKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFDTKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-15", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42927", "model_name": "GOB-15", "model_type_id": "40292"}, "3600": {"model_id": "3600", "ARO_accession": "3004806", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-14 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5798": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGGATTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTACAGGATTTCAAAACAGAAACCGGTGCAAAATTCTATACCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGACACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGTCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCCCAAGATAAATAA", "fmax": "879", "accession": "AY647252.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAT68582.1", "sequence": "MRNFATLFFLSVCLDLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYTDKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFDTKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-14", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42926", "model_name": "GOB-14", "model_type_id": "40292"}, "3607": {"model_id": "3607", "ARO_accession": "3004813", "model_param": {"blastp_bit_score": {"param_value": "480", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-6 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5805": {"dna_sequence": {"partial": "1", "sequence": "AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT", "fmax": "756", "accession": "AF189292.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAF89148.1", "sequence": "KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-6", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42933", "model_name": "GOB-6", "model_type_id": "40292"}, "3606": {"model_id": "3606", "ARO_accession": "3004812", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-5 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5804": {"dna_sequence": {"partial": "1", "sequence": "AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATACAATCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT", "fmax": "756", "accession": "AF189290.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAF89146.1", "sequence": "KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-5", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42932", "model_name": "GOB-5", "model_type_id": "40292"}, "3605": {"model_id": "3605", "ARO_accession": "3004811", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-4 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5803": {"dna_sequence": {"partial": "1", "sequence": "AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACGCTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTACGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT", "fmax": "756", "accession": "AF189293.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAF89149.1", "sequence": "KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42931", "model_name": "GOB-4", "model_type_id": "40292"}, "3466": {"model_id": "3466", "ARO_accession": "3001759", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-304 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5661": {"dna_sequence": {"partial": "0", "sequence": "ATGTATAAAAAAGTCCTTGTCGTTGCAATAGCTACTCTTTTTTTATCTGCCTGCTCTTCTAACACGGTAAAACAACATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCTCTGTTTGATCAGGCACAGACCACGGGAGTTTTAGTGATTAAGCGTGGGCAGACCGAAGAAATTTATGGCAATGATATTAAAAGAGCATCAACAGAATATGTTCCCGCCTCTACCTTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAACTGAAGTATTTAAATGGGACGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACTTTAGGCGATGCAATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCGCGAAGAATTGGACTTGATCTTATGTCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCAGACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGCCCACTTAAAATTACTCCTGAGCAAGAAACCCAATTTGCTTATGAATTAGCTAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAACAAGTCCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGCTGGTTAACTGGCTGGGTCGTTCAACCGCAAGGAGAAATTGTGGCATTCTCACTCAATTTAGAAATGAAAAAAGGAATTCCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA", "fmax": "142960", "accession": "APSC01000007.1", "fmin": "142138", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. NIPH 542", "NCBI_taxonomy_id": "1217688", "NCBI_taxonomy_cvterm_id": "42825"}, "protein_sequence": {"accession": "ENX45276.1", "sequence": "MYKKVLVVAIATLFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDIKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYELANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-304", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38159", "model_name": "OXA-304", "model_type_id": "40292"}, "3609": {"model_id": "3609", "ARO_accession": "3004815", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-8 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5807": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAAGAAAAAAAGATTCCCAAGATAAATAA", "fmax": "873", "accession": "AY348327.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAQ54756.1", "sequence": "MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKRKKDSQDK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-8", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42935", "model_name": "GOB-8", "model_type_id": "40292"}, "3608": {"model_id": "3608", "ARO_accession": "3004814", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-7 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5806": {"dna_sequence": {"partial": "1", "sequence": "AAAGAACCTGAGAATATGCCAAAAGAATGGAACCAGACTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCGTCCTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCATTTCCAATAATAAAAGGAAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCATTATGACCATACAGGCGCGTTACAGGATTTTAAAACGGAAACCGGTGCGAAATTTTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGCGGAAAATCTGATTATGAATTAGGTAAATATGGTGTGACATTTAAACCTGTTACCCCAGACAAAACATTGAAGGATCAGGATAAAATAACATTGGGAAATACAACCCTGACTTTGCTTCACCATCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGATGAAAACAGGAAATACAAGATTTTAATAGCTAATATGCCTTCCATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCAGGTATTCAGTCCGATTACGCATATACTTTCAAAGCGATGAAGAATCTGGATTTTGATATCTGGGTTGCCTCGCATGCAAGTCAGTTCGATTTGCATACCAAACGCAAAGAAGGTGACTCTTACAATCCACAGTTGTTTATGGATAAAGAGAATTATTTTAAAAGGCTCGAG", "fmax": "756", "accession": "AF189297.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAF89153.1", "sequence": "KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPVTPDKTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDENRKYKILIANMPSIIVDKKFSEVTAYPGIQSDYAYTFKAMKNLDFDIWVASHASQFDLHTKRKEGDSYNPQLFMDKENYFKRLE"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-7", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42934", "model_name": "GOB-7", "model_type_id": "40292"}, "3546": {"model_id": "3546", "ARO_accession": "3003642", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5741": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCGTGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCACCTGGGTTATGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA", "fmax": "98466", "accession": "LLNM01000004.1", "fmin": "97677", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "KSG40284.1", "sequence": "MRPLLFSALLLLSGRAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSHLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-485", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40252", "model_name": "OXA-485", "model_type_id": "40292"}, "3526": {"model_id": "3526", "ARO_accession": "3003615", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5721": {"dna_sequence": {"partial": "0", "sequence": "ATGACCGTTCGACTCTCTTCGTGCGCCCTCGGCGCAGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGCACGCAGCAGGCCTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGACTACCCCGACTGGGGCGGCGACGCTTGGCGCCAGCCCACGGATCCTGCACGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCGCGGGCGCTGGGCCAGGAACGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGATGTCTCGGGCGAACCCGGCAAGCACAACGGCACCGACGGCGCCTGGATCATCTCGTCGCTGCGCATCTCGCCGCTGGAACAGCTGGCCTTCCTGCGCAAGGTGGTCAACCGGCAGTTGCCGGTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGGCGGCTGGCGCCTGCATGGCAAGACCGGCACCGGCTCGCCGGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCTTGGTGCAGGACGAACAGGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCGCCCCGCAAGTAA", "fmax": "828", "accession": "KP903889.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter insuavis", "NCBI_taxonomy_id": "1287735", "NCBI_taxonomy_cvterm_id": "42556"}, "protein_sequence": {"accession": "ALC76101.1", "sequence": "MTVRLSSCALGAALSLSALAGAPAQAAVLCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPDYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKVVNRQLPVKAAAYDLAENLFEVGEAGGWRLHGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-459", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40225", "model_name": "OXA-459", "model_type_id": "40292"}, "3527": {"model_id": "3527", "ARO_accession": "3003616", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5722": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGACAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA", "fmax": "651807", "accession": "CP023866.1", "fmin": "651045", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "ATL95930.1", "sequence": "MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVTRRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKS"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-460", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40226", "model_name": "OXA-460", "model_type_id": "40292"}, "3524": {"model_id": "3524", "ARO_accession": "3003613", "model_param": {"blastp_bit_score": {"param_value": "555", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5719": {"dna_sequence": {"partial": "0", "sequence": "ATGACCGTTCGCCTCTTTTCGACCGCTCTCGGCGCGGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCATCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGCACGCAGCAGGCGTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGACGTCTCGGGCGAACCCGGCAAGCACAACGGCCTGGACGGCGCATGGATCAACTCGTCGCTGCGGATTTCTCCGTTGGAACAACTGGCGTTCTTGCGCAAGCTGGTCAACCGGCAATTGCCGGTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCAGCGGCTGGCACCTGTATGGCAAGACCGGCACCGGCTCGCCTGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCCCGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCCTGGTGCAGGACGAGCAGGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCGCCGCGCAAGTAA", "fmax": "828", "accession": "KP903886.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter sp. 2015clin2ach", "NCBI_taxonomy_id": "1707589", "NCBI_taxonomy_cvterm_id": "42840"}, "protein_sequence": {"accession": "ALC76098.1", "sequence": "MTVRLFSTALGAALSLSALAGAPAQAAILCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPVKAAAYDLAENLFEVGEASGWHLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-457", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40223", "model_name": "OXA-457", "model_type_id": "40292"}, "3525": {"model_id": "3525", "ARO_accession": "3003614", "model_param": {"blastp_bit_score": {"param_value": "555", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5720": {"dna_sequence": {"partial": "0", "sequence": "ATGACCGTTCGCCTCTCTTCGACCGCTCTCGGCGCGGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGTACGCAGCAGGCCTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGACGTCTCGGGCGAACCCGGCAAACACAACGGCCTGGACGGCGCATGGATCAACTCGTCGCTGCGGATTTCTCCGTTGGAACAACTGGCGTTCTTGCGCAAGCTGGTCAACCGGCAATTGCCGCTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGGCGGCTGGCGTATGCACGGCAAGACCGGCACCGGCTCGCCTGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCACGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCTTGGTGCAGGACGAGCAAGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCACCGCGCAAGTAA", "fmax": "828", "accession": "KP903888.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter sp. 2015clin4ach", "NCBI_taxonomy_id": "1707590", "NCBI_taxonomy_cvterm_id": "42841"}, "protein_sequence": {"accession": "ALC76100.1", "sequence": "MTVRLSSTALGAALSLSALAGAPAQAAVLCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKAAAYDLAENLFEVGEAGGWRMHGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-458", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40224", "model_name": "OXA-458", "model_type_id": "40292"}, "3522": {"model_id": "3522", "ARO_accession": "3003609", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5717": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGGAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG", "fmax": "774", "accession": "KR061507.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29919.1", "sequence": "MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGGKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-453", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40219", "model_name": "OXA-453", "model_type_id": "40292"}, "3523": {"model_id": "3523", "ARO_accession": "3003611", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5718": {"dna_sequence": {"partial": "0", "sequence": "ATGACCGTTCGACGTTTTTCGTGCGCCCTGGGCGCAGCCCTTTCCCTGTCCGCGCTGGCGGGCGCCCCCGCCCGCGCCGCGGTTTTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTTCCAGCAAGGCACGCAGGCGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCGATCGCGCTGATGGGCGCGGACGCGGGCATCCTGCAAGGCCCGCACGCGCCGGTCTGGAACTACCAGCCGGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCGACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCAGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACGCCTCGGCCTTCCAGTACGGCAACGAGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCCTGGATGGCGCGTGGATCAACTCGTCGCTGCGCATTTCGCCGCTGGAGCAACTGGCGTTCCTGCGCAAGCTGGTCAACCGGCAATTGCCGCTCAAGCCCGCGGCCTACGATCTGGCCGAGACGCTGTTCGACGCCGGCGAGGCCGGCGGCTGGCGCCTGTATGGCAAGACCGGCACCGGCTCGCCCGGCGGCAACGGCGTCTACACACCGGACAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCCTGCTGCAGGACGAGAAGGCCACCAGGCCCAACGCCGGCCTGCGCGCCCGCGATGACCTGATGCGCGACTGGCCGGCCATGGCCGACGCGCCCCGCCAGTAG", "fmax": "828", "accession": "KP903885.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Achromobacter insuavis", "NCBI_taxonomy_id": "1287735", "NCBI_taxonomy_cvterm_id": "42556"}, "protein_sequence": {"accession": "ALC76097.1", "sequence": "MTVRRFSCALGAALSLSALAGAPARAAVLCTVVADAADGRIVFQQGTQAACAERYTPASTFKLPIALMGADAGILQGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFQYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKPAAYDLAETLFDAGEAGGWRLYGKTGTGSPGGNGVYTPDNAYGWFVGWARKDGRQLVFARLLQDEKATRPNAGLRARDDLMRDWPAMADAPRQ"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-455", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40221", "model_name": "OXA-455", "model_type_id": "40292"}, "3520": {"model_id": "3520", "ARO_accession": "3003607", "model_param": {"blastp_bit_score": {"param_value": "514", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5715": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGTACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG", "fmax": "774", "accession": "KR061504.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29916.1", "sequence": "MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIVLDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-451", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40217", "model_name": "OXA-451", "model_type_id": "40292"}, "3521": {"model_id": "3521", "ARO_accession": "3003608", "model_param": {"blastp_bit_score": {"param_value": "513", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5716": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATATAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG", "fmax": "774", "accession": "KR061505.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29917.1", "sequence": "MKKITLFLLFLNLVFGQDKILNNWFKEYNISGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-452", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40218", "model_name": "OXA-452", "model_type_id": "40292"}, "3528": {"model_id": "3528", "ARO_accession": "3003617", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5723": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTTAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA", "fmax": "762", "accession": "KR061509.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29921.1", "sequence": "MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFLRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKS"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-461", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40227", "model_name": "OXA-461", "model_type_id": "40292"}, "3529": {"model_id": "3529", "ARO_accession": "3003620", "model_param": {"blastp_bit_score": {"param_value": "480", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5724": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAAAAAATAAAACTAATTTTTATTTTAATTTTTTCAATAAATTTATTTGCAAATGATGTGGAACTTGAAAATTTATTTAAAAAATACCAAGTTGAAGGAACTTTAGTATTAGAGTCTTTAAATACAAAAAAAGTAGATATTTATAATGAAAAGCGAGCAAATACATCGTTTTCTCCTGCTTCAACATTTAAAATACCAAATACTTTGATAGCTTTAAATGAAGGTGTTGTAAACAAAGATTCTATAATAGTTTGGGATAAAAAAGTAAGAGAATTTGATGCTTGGAATAAAGACCAAACTTTACAATCAGCTTTCAAAAGTTCATGCGTTTGGTGTTATAAAGAGTTCGCTTCAAAAATTGGAGTTGAAAAATATAAAAAGTATCTAAAAGAGCTTAATTATGGAAATAAAACAATAGGCAAAGATGTAACTGATTTTTGGTTGGATGAGAGTTTGAGAATTACAGCTTTTGAAGAGATAAGATTTTTAAAACAATTACAAGCAAACAATTTAGCTTTTAAACAAGAAGATATAAATCTTTTAAAAGAGTTGATGATTGATGAAAAAAGCGAAAATTATGTAGTTAGAGCAAAAACAGGTTGGGAAGGAAAATATGGTTGGTATGTTGGTTATGTTGAAACAAAAAATGATGTTTGGTTTTTTGCTTTAAATATCGACACAAAAACAAAAGAAGATTTAGCAAAAAGAAAAGCTTTAACTTTAGAAGCTTTAAAAACAAAAGGGATTATAGATTGA", "fmax": "762", "accession": "KU721146.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Arcobacter butzleri", "NCBI_taxonomy_id": "28197", "NCBI_taxonomy_cvterm_id": "42842"}, "protein_sequence": {"accession": "ANW35663.1", "sequence": "MNKKIKLIFILIFSINLFANDVELENLFKKYQVEGTLVLESLNTKKVDIYNEKRANTSFSPASTFKIPNTLIALNEGVVNKDSIIVWDKKVREFDAWNKDQTLQSAFKSSCVWCYKEFASKIGVEKYKKYLKELNYGNKTIGKDVTDFWLDESLRITAFEEIRFLKQLQANNLAFKQEDINLLKELMIDEKSENYVVRAKTGWEGKYGWYVGYVETKNDVWFFALNIDTKTKEDLAKRKALTLEALKTKGIID"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-464", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40230", "model_name": "OXA-464", "model_type_id": "40292"}, "3449": {"model_id": "3449", "ARO_accession": "3001739", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-284 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5645": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAACTCTGATTTTTCTGCCTTTACTTAATTGCTTGAGCCTGACGGCGTGTACCTTACCCGTTTCATCTTCCCCATCTCATATCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCTCTGGCGTTTTAGTGATTCAGCGTGGTCAACAGATACAGGTCTATGGCAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGTAAGAAACGCAGTTTTTCAGCCTGGGAAAAAGATATGACTCTCGGTGAAGCCATGCAAGCGTCTGCTGTACCCGTCTATCAGGAACTGGCGCGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA", "fmax": "73515", "accession": "APRU01000004.1", "fmin": "72684", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. CIP 51.11", "NCBI_taxonomy_id": "1144670", "NCBI_taxonomy_cvterm_id": "42810"}, "protein_sequence": {"accession": "ENX16434.1", "sequence": "MKTLIFLPLLNCLSLTACTLPVSSSPSHITSTQSTQAIAQLFDQAQSSGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-284", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38139", "model_name": "OXA-284", "model_type_id": "40292"}, "3448": {"model_id": "3448", "ARO_accession": "3001738", "model_param": {"blastp_bit_score": {"param_value": "510", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-283 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5644": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAATTCTAATTTTGCTGCCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTAGCCTGCCCGTTTCATCTCTCCTATCTCAAAGCACTTCGACTCAATCCACCCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCGGGTGTTCTAGTGATTCAGCGTGGTCAACAGATACAGGTTTATGGTAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAATTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAAGCCGAGATCGTGGCATTTTCACTGAATATGCAGATGCGAAATGGTATGGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA", "fmax": "115730", "accession": "APOG01000008.1", "fmin": "114899", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter sp. CIP A162", "NCBI_taxonomy_id": "1144674", "NCBI_taxonomy_cvterm_id": "42809"}, "protein_sequence": {"accession": "ENU15301.1", "sequence": "MKILILLPLLSCLGLTACSLPVSSLLSQSTSTQSTQAIAQLFDQAQSAGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMRNGMDPAIRLEILQQALAELGLYPKAEG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-283", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38138", "model_name": "OXA-283", "model_type_id": "40292"}, "3445": {"model_id": "3445", "ARO_accession": "3001735", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-280 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5641": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAACTTTACAGTTGGGCCTCATCGTCCTCATTACTACCTTCGGTTCTGCATGTACCATAATAAGAAGCCCCTCCATAGAAACAGCTAAAAACCATGAGCAACAAAGTGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACGGGGGTGATTGTCATAAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTGTTTAAATGGGATGGTCAAAAGAACAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCTGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGATCTAATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGAATAATTTAA", "fmax": "8353", "accession": "APPZ01000001.1", "fmin": "7525", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter johnsonii ANC 3681", "NCBI_taxonomy_id": "1217662", "NCBI_taxonomy_cvterm_id": "42807"}, "protein_sequence": {"accession": "ENV74419.1", "sequence": "MKTLQLGLIVLITTFGSACTIIRSPSIETAKNHEQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKNSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-280", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38135", "model_name": "OXA-280", "model_type_id": "40292"}, "3444": {"model_id": "3444", "ARO_accession": "3001734", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-279 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5640": {"dna_sequence": {"partial": "0", "sequence": "ATGCCAAAAATACTAAAACATCTTGGCCTTTGCGCATCTGTAATGATTGGACTGACGTTGCTAGGTTGCCAAAATTTGCAGGCCCCAACTCAAAGCGCCGTGTCAAAAAAACACGACCAAACCGAGATCGCTTCTTTATTCCAACATGCTCAAACTGTTGGCGTATTTGTTACATATGATGGGCAAACACTTCAAGAATATGGCAATGCGCTGAGTCGATCGAATACAGCTTATATTCCAGCCTCAACTTTCAAGATGTTAAATGCTCTGATTGGGATACAGCATCACAAAAGTTCGCCAAACGAAGTGTTTAAATGGGATGGCAAAAAGCGTGCTTTTGCGAGCTGGGAAAAAGATTTAACCTTAGCTGAGGCGATGCAGGCATCGGCAGTGCCTGTTTATCAAGAATTGGCTCGACGTATTGGTTTAGAGCTGATGGCGAACGAAGTGAAGCGAGTGGGCTTTGGCAATGCTGAGATCGGAACGCAAGTCGATGATTTTTGGTTGGTTGGTCCACTGAAGATTACCCCCGTTGAAGAAGTCAAATTTGCTTATGCTTTGGCTCATAAGCAGCTTACATTTGATCAATCTGTGCAGGAACAAGTGAAACAGATGGTTTTGGTTGATGAAGTTAAAGGAACCAAAATTTATGCCAAAAGTGGTTGGGGTATGGATGTAACGCCCCAAGTAGGTTGGTGGACAGGCTGGATTGAGCAACCGAATGGGCAGGTGATTGCATTTTCTTTAAATATGCAAATAAATAATTCTAAGCAGGGCGATGCGCGTAAAGCGATTGTTTATCAGGCATTACAACAATTGAAATTGTTAGAGACGCAATAA", "fmax": "55702", "accession": "APOM01000058.1", "fmin": "54862", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter parvus DSM 16617 = CIP 108168", "NCBI_taxonomy_id": "981333", "NCBI_taxonomy_cvterm_id": "41200"}, "protein_sequence": {"accession": "ENU35234.1", "sequence": "MPKILKHLGLCASVMIGLTLLGCQNLQAPTQSAVSKKHDQTEIASLFQHAQTVGVFVTYDGQTLQEYGNALSRSNTAYIPASTFKMLNALIGIQHHKSSPNEVFKWDGKKRAFASWEKDLTLAEAMQASAVPVYQELARRIGLELMANEVKRVGFGNAEIGTQVDDFWLVGPLKITPVEEVKFAYALAHKQLTFDQSVQEQVKQMVLVDEVKGTKIYAKSGWGMDVTPQVGWWTGWIEQPNGQVIAFSLNMQINNSKQGDARKAIVYQALQQLKLLETQ"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-279", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38134", "model_name": "OXA-279", "model_type_id": "40292"}, "3447": {"model_id": "3447", "ARO_accession": "3001737", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-282 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5643": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAATTCTGATTTTGCTGCCTTTACTTAGTTGCTTGGGCCTGACAGCGTGTAGCCTGCCCGTTTCATCTCTCCTATCTCAAAGCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCGGGTGTTCTAGTGATTCAGCGTGGTCAACAGATACAGGTTTATGGTAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAATTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA", "fmax": "901", "accession": "AMFJ01001993.1", "fmin": "70", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "EKE23052.1", "sequence": "MKILILLPLLSCLGLTACSLPVSSLLSQSTSTQSTQAIAQLFDQAQSAGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-282", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38137", "model_name": "OXA-282", "model_type_id": "40292"}, "3446": {"model_id": "3446", "ARO_accession": "3001736", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-281 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5642": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAACTTTACAATTTGGACTCATCGCCCTCATTACAACCTTCGGTTCTGCATGTACCACAATAAGCCCCTCAGTAGAAACAGCTAAAAATCACCAGCAACAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGAACCGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGTATTGGTCTAGACCTGATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTGAGCCAGATGTGCAACATACCGTACAAGACATGTTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCAGATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGATAACACTGGGGATAATTTAA", "fmax": "11268", "accession": "APON01000041.1", "fmin": "10443", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter johnsonii CIP 64.6", "NCBI_taxonomy_id": "1217663", "NCBI_taxonomy_cvterm_id": "42808"}, "protein_sequence": {"accession": "ENU38533.1", "sequence": "MKTLQFGLIALITTFGSACTTISPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATRTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFEPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMQMKTGISASVREQLVKQSLITLGII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-281", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38136", "model_name": "OXA-281", "model_type_id": "40292"}, "3441": {"model_id": "3441", "ARO_accession": "3001731", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-275 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5637": {"dna_sequence": {"partial": "0", "sequence": "ATGAGTAATTACCGATTTAAATCTAAAATAAAAAGCAGTGTATTGATCATTCTGAGTAGTGTGGCATTTTCAGGTTGTGTTTCTAATGCCAATTTGCATGATCCAGCGTCATCACAAAGAACAAGTGAAATCCCGTTGTTGTTTAATTATGCGCAAACTCAAGCCGTCTTTGTGACTTATGATGGAACTCAATTTAAACGTTATGGGAATGATTTAAATAGAGCCAAGACTGCCTATATTCCAGCCTCTACTTTTAAAATGTTGAATGCCTTAATTGGTTTGCAACATGCGAAAGCGACGAATACAGAAGTATTTAAGTGGAATGGAGAAAAAAGATCTTTTCCTGCATGGGAAAAAGATATGACCTTGGCACAAGCAATGCAGGCTTCAGCCGTACCTGTATATCAGGAGTTGGCACGACGTATTGGCTTGGATTTGATGAGTAAAGAAGTCAAGCGTGTTGGTTTTGGCAATACACAAATTGGTCAACAGGTAGATAATTTCTGGCTAGTCGGCCCATTGAAAATTACCCCAGAGCAAGAAGCTAAATTTGCTTTTCAATTGGCAAACAAAACATTGCCTTTTGATGATGCTGTACAGCAACAAGTTAAAGATATGCTCTATGTCGAAAGACGGGGTGATTCCAAGCTTTATGCCAAAAGTGGATGGGGAATGGATGTGGAGCCACAAGTGGGTTGGTATACGGGATGGGTGGAACAGCCGAATGGTCAGATCACCGCTTTTGCTTTAAACATGCACATGCAGACAGGGGATGATCCTGCTGAACGCAAGCAACTGACATTAAGTATCTTGGATAAATTAGGCTTATTCTTTTATTTGAGATAA", "fmax": "18073", "accession": "APPJ01000001.1", "fmin": "17227", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter guillouiae NIPH 991", "NCBI_taxonomy_id": "1217656", "NCBI_taxonomy_cvterm_id": "42804"}, "protein_sequence": {"accession": "ENV18923.1", "sequence": "MSNYRFKSKIKSSVLIILSSVAFSGCVSNANLHDPASSQRTSEIPLLFNYAQTQAVFVTYDGTQFKRYGNDLNRAKTAYIPASTFKMLNALIGLQHAKATNTEVFKWNGEKRSFPAWEKDMTLAQAMQASAVPVYQELARRIGLDLMSKEVKRVGFGNTQIGQQVDNFWLVGPLKITPEQEAKFAFQLANKTLPFDDAVQQQVKDMLYVERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGQITAFALNMHMQTGDDPAERKQLTLSILDKLGLFFYLR"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-275", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38131", "model_name": "OXA-275", "model_type_id": "40292"}, "3440": {"model_id": "3440", "ARO_accession": "3001729", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-273 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5636": {"dna_sequence": {"partial": "0", "sequence": "ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACATGGGCGAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGGTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCAACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCAGAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATCTAGAAATGGAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTACTTATAAGGGATTGGAACAACTCGGTATTTTATAA", "fmax": "1170954", "accession": "APQN01000012.1", "fmin": "1170132", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter pittii ANC 3678", "NCBI_taxonomy_id": "1217673", "NCBI_taxonomy_cvterm_id": "42803"}, "protein_sequence": {"accession": "ENW12288.1", "sequence": "MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKHGRTEEVYGNDLKRASTEYVPASTFKMVNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEVQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPEVGWFTGWVVQPQGEIIAFSLNLEMEKGIPSSIRKEITYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-273", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38129", "model_name": "OXA-273", "model_type_id": "40292"}, "3443": {"model_id": "3443", "ARO_accession": "3001733", "model_param": {"blastp_bit_score": {"param_value": "510", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-277 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5639": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAATTCTTATTTTGTGGCCTTTACTCAGTTGCTTGAGCCTGACAGCTTGTAGCTTCGCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTACTGCAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATGTTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATTTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGTATTCAATTTGGTAATCAGCAGATTGGTCATCAGGTCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGAAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAGCTTGCCTTTGATCCTCGGGTTCAGCAGCAAGTTAAAACCATGTTACTGTTACAGGAGCGACAAGCTTATCGGCTTTATGCTAAATCCGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATTGAAACACCTCAGGACGAAATCGTGGTATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCTGAATTAGGGCTTTATCCGAAAGCTGAAGCGTAA", "fmax": "9991", "accession": "APPQ01000011.1", "fmin": "9160", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter schindleri CIP 107287", "NCBI_taxonomy_id": "1217988", "NCBI_taxonomy_cvterm_id": "42806"}, "protein_sequence": {"accession": "ENV45890.1", "sequence": "MKILILWPLLSCLSLTACSFAVSNSPSQITSTQSIQATAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYVPASTFKMFNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGHQVDNFWLVGPLKITPKQEVEFASALAQEQLAFDPRVQQQVKTMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVVFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEA"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-277", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38133", "model_name": "OXA-277", "model_type_id": "40292"}, "3442": {"model_id": "3442", "ARO_accession": "3001732", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-276 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5638": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAATTCTTATTTTGTGGCCTTTACTCAGTTACTTGAGCCTGACAGCCTGTAGCTTCCCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTATTGCAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATATTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATTTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTACAACGTATTCAATTTGGTAATCAGCAGATTGGTCATCAGGTCGACAACTTCTGGTTAGTCGGACCTTTGAAAGTCACCCCGAAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAGCTTGCCTTTGATCCTCGGGTTCAGCAGCAAGTTAAAACCATGTTACTGTTACAGGAGCGACAAGCTTATCGGCTTTATGCTAAATCCGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGTTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGACTTTATCCAAAAGCTGAAGGGTGA", "fmax": "55474", "accession": "APPI01000013.1", "fmin": "54643", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter schindleri NIPH 900", "NCBI_taxonomy_id": "1217675", "NCBI_taxonomy_cvterm_id": "42805"}, "protein_sequence": {"accession": "ENV13583.1", "sequence": "MKILILWPLLSYLSLTACSFPVSNSPSQITSTQSIQAIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYVPASTFKIFNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGHQVDNFWLVGPLKVTPKQEVEFASALAQEQLAFDPRVQQQVKTMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-276", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38132", "model_name": "OXA-276", "model_type_id": "40292"}, "3602": {"model_id": "3602", "ARO_accession": "3004808", "model_param": {"blastp_bit_score": {"param_value": "490", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-16 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5800": {"dna_sequence": {"partial": "0", "sequence": "ATGAGAAACTTTGCAATTTTATTTTTTTTACTAATCACTTTCAGCTGGAAAGCTCAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATGAGCCATTCAGAATTGCGGGTAACTTATACTATGTAGGAACTTACGATCTGGCTTCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCTGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATTAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAAACAGAAACAGGTGCGAAATTTTATGCAGACAGTGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGCCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTATAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCGAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCCTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA", "fmax": "873", "accession": "GU188443.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "ACZ72746.1", "sequence": "MRNFAILFFLLITFSWKAQVVKEPENTNEEWSRSYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKFYADSADADVLKTGGKSDYEMGKYGATFKPIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDPYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-16", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42928", "model_name": "GOB-16", "model_type_id": "40292"}, "3548": {"model_id": "3548", "ARO_accession": "3003645", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5743": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCGGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA", "fmax": "18008", "accession": "SMRY02000082.1", "fmin": "17219", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "TKV86805.1", "sequence": "MRPLLFSALLLLSGHAQASEWNDSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-488", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40255", "model_name": "OXA-488", "model_type_id": "40292"}, "3549": {"model_id": "3549", "ARO_accession": "3004734", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "ARL-1 is a beta-lactamase gene found in Staphylococcus Arlettae.", "model_sequences": {"sequence": {"5744": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACTTTTAAAGCCATTACGAGTGGGTTATTATTACAGCAAAATTCTCCTGAAGCATTAAACAAAACTGTAACGATAAAAGAATCAGATATCGTGGCGTATTCACCTGTTACCGAACAATATGTCGGAAAAACCATGACCCTACGCCAATTAATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAACAACTCGGTGGTCTAGATCAGCTTTCGTCTCGCTTACAAGCACTCGGTGACACAACAACAAACCCACAACGTTATGAACCCGAATTAAATAACTATGATCCACAAAGTACGGCAGATACATCAACACCTCGTGCTACTGCCCATAATTTGCAAAAACTATTAACAACAGATGCCGTTGCACCACAACAGCGTAAGTTTTTACAAAATTTAATGTTCAACAATAAAACAGGTGAGAGTTTAATCAAAAAAGGTGTCCCTAACAGTTATAAAGTAGGTGACAAAAGTGGCCAAGGTACAACTTATGGCACGCGTAATGATGTTGCCGTCATCTATCCAAAACATCAAACAAAACCAATTATTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA", "fmax": "80337", "accession": "KY363215.1", "fmin": "79488", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus arlettae", "NCBI_taxonomy_id": "29378", "NCBI_taxonomy_cvterm_id": "42844"}, "protein_sequence": {"accession": "APY23733.1", "sequence": "MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQNSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQLSSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHNLQKLLTTDAVAPQQRKFLQNLMFNNKTGESLIKKGVPNSYKVGDKSGQGTTYGTRNDVAVIYPKHQTKPIILVVFTKHQQQDAQPQDELVAQAARHAIHQLD"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42853": {"category_aro_name": "ARL Beta-lactamase", "category_aro_cvterm_id": "42853", "category_aro_accession": "3004742", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae."}}, "ARO_name": "ARL-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42843", "model_name": "ARL-1", "model_type_id": "40292"}, "3531": {"model_id": "3531", "ARO_accession": "3003622", "model_param": {"blastp_bit_score": {"param_value": "450", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5726": {"dna_sequence": {"partial": "0", "sequence": "TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGATCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA", "fmax": "747", "accession": "KR061501.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29913.1", "sequence": "MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLRSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-466", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40232", "model_name": "OXA-466", "model_type_id": "40292"}, "3530": {"model_id": "3530", "ARO_accession": "3003621", "model_param": {"blastp_bit_score": {"param_value": "440", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5725": {"dna_sequence": {"partial": "0", "sequence": "TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATGATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAACGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCTTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTCGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA", "fmax": "747", "accession": "KR061500.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AKI29912.1", "sequence": "MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNDFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKDIKNIKIREELLEKYIYSLN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-465", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40231", "model_name": "OXA-465", "model_type_id": "40292"}, "3533": {"model_id": "3533", "ARO_accession": "3003627", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5728": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTCGAATCTTGGGCTAAAGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTATTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182164.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79286.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAISDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-471", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40237", "model_name": "OXA-471", "model_type_id": "40292"}, "3532": {"model_id": "3532", "ARO_accession": "3003626", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5727": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATAAATTCAGATGACCTTGCAAAAAGGATAAATATAGAAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182163.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79285.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIEKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-470", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40236", "model_name": "OXA-470", "model_type_id": "40292"}, "3535": {"model_id": "3535", "ARO_accession": "3003629", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5730": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATTTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTATTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182166.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79288.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLEFWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAISDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-473", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40239", "model_name": "OXA-473", "model_type_id": "40292"}, "3534": {"model_id": "3534", "ARO_accession": "3003628", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5729": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACTAAGATTTTATCAAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "807", "accession": "KR182165.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79287.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAELRFYQASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-472", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40238", "model_name": "OXA-472", "model_type_id": "40292"}, "3537": {"model_id": "3537", "ARO_accession": "3003632", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5732": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTGAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAGGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182168.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79290.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSENMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKEGLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-475", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40242", "model_name": "OXA-475", "model_type_id": "40292"}, "3536": {"model_id": "3536", "ARO_accession": "3003631", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5731": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATGTATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATTTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182167.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79289.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNVFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLEFWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-474", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40241", "model_name": "OXA-474", "model_type_id": "40292"}, "3539": {"model_id": "3539", "ARO_accession": "3003634", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5734": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATGTATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATATTGGCGAAAAAGTTTTTCTTGAATTTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTGAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182170.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79292.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNVFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYIGEKVFLEFWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVELLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-477", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40244", "model_name": "OXA-477", "model_type_id": "40292"}, "3538": {"model_id": "3538", "ARO_accession": "3003633", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5733": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAATGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTGAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182169.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79291.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDNVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSENMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-476", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40243", "model_name": "OXA-476", "model_type_id": "40292"}, "3507": {"model_id": "3507", "ARO_accession": "3003593", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5702": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCTCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA", "fmax": "828", "accession": "KP410856.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AKL59536.1", "sequence": "MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKISFSLNLEMKEGMSGSIRNEITYKSLENLGII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-437", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40203", "model_name": "OXA-437", "model_type_id": "40292"}, "3438": {"model_id": "3438", "ARO_accession": "3001727", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-271 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5634": {"dna_sequence": {"partial": "0", "sequence": "ATGACTAAAAAAGCTCTTTTCCTTGCTATTAGTACTATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACGCTCTTTCTACCCATAAAAATTCAGAAGAAATTCAATCACTGTTTGATCAAGCGCAGACCACCGGTGTTTTGGTTATTAAGCGTGGAAAAAAAGAGGAAATTTATGGCAATGATCTAAAAAGAGCATCAACTGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTCAAATGGGACGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAAGATATGACCTTAGGCGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGATCAAGCGTGTGGATTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTTGTTCAACAACAAGGAGAAATTGTAGCTTTCTCACTCAATTTAGAAATGAAAAAAGGAATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA", "fmax": "135802", "accession": "APQO01000006.1", "fmin": "134980", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter lactucae", "NCBI_taxonomy_id": "1785128", "NCBI_taxonomy_cvterm_id": "42801"}, "protein_sequence": {"accession": "EOQ72432.1", "sequence": "MTKKALFLAISTIFLSACSFNTVQQHQIHALSTHKNSEEIQSLFDQAQTTGVLVIKRGKKEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEIKRVDFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQQQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-271", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38127", "model_name": "OXA-271", "model_type_id": "40292"}, "3439": {"model_id": "3439", "ARO_accession": "3001728", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-272 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5635": {"dna_sequence": {"partial": "0", "sequence": "ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGTAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATAGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGTATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACCTTAGGTGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGTACGGTTTGCTTACAAATTAGCCAACAAAACTCTTCCCTTTAGTAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCTCAAGTGGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAG", "fmax": "307073", "accession": "APQP01000003.1", "fmin": "306251", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter pittii ATCC 19004 = CIP 70.29", "NCBI_taxonomy_id": "1311774", "NCBI_taxonomy_cvterm_id": "42802"}, "protein_sequence": {"accession": "ENW16915.1", "sequence": "MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWYGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEVRFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-272", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38128", "model_name": "OXA-272", "model_type_id": "40292"}, "3430": {"model_id": "3430", "ARO_accession": "3001719", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-263 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5626": {"dna_sequence": {"partial": "0", "sequence": "ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACCGCTAATCCAAATTACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACAAACTAGGGGTGTTTTAGTTATCCAACAAGGTCAAATTCAACAAAGTTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTTAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAAAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGCGTTGGTTATGGCAATGCAGATATAGGCACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTCGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "417423", "accession": "APQY01000006.1", "fmin": "416598", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii NIPH 329", "NCBI_taxonomy_id": "1217632", "NCBI_taxonomy_cvterm_id": "42794"}, "protein_sequence": {"accession": "ENW43915.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNYSASKSDEKAEKIKNLFNEAQTRGVLVIQQGQIQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWNGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-263", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38119", "model_name": "OXA-263", "model_type_id": "40292"}, "3431": {"model_id": "3431", "ARO_accession": "3001720", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-264 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5627": {"dna_sequence": {"partial": "0", "sequence": "ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTTGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGTATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAACGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCGAAACAGGAGTTACCATTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACTCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA", "fmax": "287728", "accession": "APQQ01000012.1", "fmin": "286900", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter haemolyticus CIP 64.3", "NCBI_taxonomy_id": "1217659", "NCBI_taxonomy_cvterm_id": "42795"}, "protein_sequence": {"accession": "ENW20318.1", "sequence": "MKLSKLYTLTVLIGFGLSGVACQHIHTPVLFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-264", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38120", "model_name": "OXA-264", "model_type_id": "40292"}, "3432": {"model_id": "3432", "ARO_accession": "3001721", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-265 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5628": {"dna_sequence": {"partial": "0", "sequence": "ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAGCTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCAAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACCCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA", "fmax": "1357462", "accession": "PXZD01000001.1", "fmin": "1356634", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter haemolyticus", "NCBI_taxonomy_id": "29430", "NCBI_taxonomy_cvterm_id": "36938"}, "protein_sequence": {"accession": "RFX69805.1", "sequence": "MKLSKLYTLTVLIGFGLSGVACQHIHTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKAAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-265", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38121", "model_name": "OXA-265", "model_type_id": "40292"}, "3604": {"model_id": "3604", "ARO_accession": "3004810", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "GOB-3 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.", "model_sequences": {"sequence": {"5802": {"dna_sequence": {"partial": "1", "sequence": "AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCATTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCTAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTACATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTTCAAAACCTTAAT", "fmax": "756", "accession": "AF189291.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Elizabethkingia meningoseptica", "NCBI_taxonomy_id": "238", "NCBI_taxonomy_cvterm_id": "36960"}, "protein_sequence": {"accession": "AAF89147.1", "sequence": "KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYLNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "41376": {"category_aro_name": "GOB beta-lactamase", "category_aro_cvterm_id": "41376", "category_aro_accession": "3004212", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}, "ARO_name": "GOB-3", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42930", "model_name": "GOB-3", "model_type_id": "40292"}, "3434": {"model_id": "3434", "ARO_accession": "3001723", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-267 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5630": {"dna_sequence": {"partial": "0", "sequence": "ATGTATAAAAAAGCCCTTATCGCTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCATGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCTATTTGCTTATCAATTAGCTCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAATCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA", "fmax": "1454995", "accession": "APQH01000006.1", "fmin": "1454173", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter calcoaceticus ANC 3680", "NCBI_taxonomy_id": "1217653", "NCBI_taxonomy_cvterm_id": "42797"}, "protein_sequence": {"accession": "ENV93423.1", "sequence": "MYKKALIAATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTMGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETLFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQSQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-267", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38123", "model_name": "OXA-267", "model_type_id": "40292"}, "3435": {"model_id": "3435", "ARO_accession": "3001724", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-268 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5631": {"dna_sequence": {"partial": "0", "sequence": "ATGTATAAAAAAGCGCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAACATCAAATACACTCTATGTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAAACCACGGGTGTTTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGCCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTAATGCGATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCTAAAGAGGTAAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACGCCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAGATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATATTATAA", "fmax": "972910", "accession": "APOE01000008.1", "fmin": "972088", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter calcoaceticus NIPH 13", "NCBI_taxonomy_id": "1217654", "NCBI_taxonomy_cvterm_id": "42798"}, "protein_sequence": {"accession": "ENU09033.1", "sequence": "MYKKALIVTTSILFLSACSSNSVKQHQIHSMSANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGNAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-268", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38124", "model_name": "OXA-268", "model_type_id": "40292"}, "3436": {"model_id": "3436", "ARO_accession": "3001725", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-269 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5632": {"dna_sequence": {"partial": "0", "sequence": "ATGTATAAAAAAGTCCTTATCGTGGCAACAACTACTCTATTTTTATCTGCCTGCTCTTCTAAGACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATCAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCGCAGACTACGGGGGTTTTGGTGATTAAGCGTGGGCAAACAGAAGAAATTTATGGTAATGATTTGAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATATTGAATGCTTTAATTGGACTTGAACATCATAAGGTAACAACAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGCAAGCTTCTGCTATTCCAGTTTATCAAAAATTAGCCCGAAGAATTGGCCTGGATCTTATGTCTAAAGAGGTGAAACGAGTTGGTTTCGGTAATGCGGACATTGGTTCACGAGTAGATAATTTTTGGCTTGTTGGTCCACTCAAAATTACACCTCTGCAAGAAGCCGAATTTGCTTATGAATTAGCTCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAGTCACTGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTACGCAAAAAGTGGTTGGGCATTGGATATTGATCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCATTATTCGTAAAGAAATTACTTATAAAGGATTAGAACAACTGGGTATCTTATAA", "fmax": "350155", "accession": "APQJ01000007.1", "fmin": "349333", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter calcoaceticus ANC 3811", "NCBI_taxonomy_id": "1217690", "NCBI_taxonomy_cvterm_id": "42799"}, "protein_sequence": {"accession": "EOQ63861.1", "sequence": "MYKKVLIVATTTLFLSACSSKTVKQHQIHSISANQNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKILNALIGLEHHKVTTTEVFKWDGQKRLFPDWEKDMTLGDAMQASAIPVYQKLARRIGLDLMSKEVKRVGFGNADIGSRVDNFWLVGPLKITPLQEAEFAYELAHKTLPFSKNVQEQVQSLVFIEEKNGRKIYAKSGWALDIDPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSIIRKEITYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-269", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38125", "model_name": "OXA-269", "model_type_id": "40292"}, "3437": {"model_id": "3437", "ARO_accession": "3001726", "model_param": {"blastp_bit_score": {"param_value": "560", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-270 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5633": {"dna_sequence": {"partial": "0", "sequence": "ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACATCACCAAATACACGCTATTTCTACTCATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGGGCATCAACTGAATATGTCCCTGCATCTACCTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACCACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTATCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA", "fmax": "257164", "accession": "APQM01000006.1", "fmin": "256342", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter pittii ANC 4050", "NCBI_taxonomy_id": "1217691", "NCBI_taxonomy_cvterm_id": "42800"}, "protein_sequence": {"accession": "EOQ69512.1", "sequence": "MTKKALFFAISTIFLSACSFNTVQHHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLIGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-270", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38126", "model_name": "OXA-270", "model_type_id": "40292"}, "3579": {"model_id": "3579", "ARO_accession": "3004778", "model_param": {"blastp_bit_score": {"param_value": "740", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "CMY-135 is a class C beta-lactamase that confers resistance to cephamycin.", "model_sequences": {"sequence": {"5777": {"dna_sequence": {"partial": "0", "sequence": "ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCTAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA", "fmax": "1146", "accession": "KP981366.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Citrobacter freundii", "NCBI_taxonomy_id": "546", "NCBI_taxonomy_cvterm_id": "36915"}, "protein_sequence": {"accession": "AKP17985.1", "sequence": "MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHLVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36208": {"category_aro_name": "CMY beta-lactamase", "category_aro_cvterm_id": "36208", "category_aro_accession": "3000069", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins 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. The 7-alpha-methoxy group increases resistance to beta-lactamases."}}, "ARO_name": "CMY-135", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42893", "model_name": "CMY-135", "model_type_id": "40292"}, "3578": {"model_id": "3578", "ARO_accession": "3003653", "model_param": {"blastp_bit_score": {"param_value": "750", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From Lahey's list of beta-lactamases, no additional information available", "model_sequences": {"sequence": {"5776": {"dna_sequence": {"partial": "0", "sequence": "ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAACGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA", "fmax": "1146", "accession": "KP862819.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AKZ20821.1", "sequence": "MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGNDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36208": {"category_aro_name": "CMY beta-lactamase", "category_aro_cvterm_id": "36208", "category_aro_accession": "3000069", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins 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. The 7-alpha-methoxy group increases resistance to beta-lactamases."}}, "ARO_name": "CMY-133", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40263", "model_name": "CMY-133", "model_type_id": "40292"}, "3544": {"model_id": "3544", "ARO_accession": "3003640", "model_param": {"blastp_bit_score": {"param_value": "545", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5739": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTGTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA", "fmax": "905", "accession": "KP264125.1", "fmin": "83", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AKF41840.1", "sequence": "MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAVALNMEMRSEMPASIRNELLMKSLKQLNII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-483", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40250", "model_name": "OXA-483", "model_type_id": "40292"}, "3545": {"model_id": "3545", "ARO_accession": "3003641", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5740": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG", "fmax": "798", "accession": "KR401105.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "ALI16502.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-484", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40251", "model_name": "OXA-484", "model_type_id": "40292"}, "3429": {"model_id": "3429", "ARO_accession": "3001718", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-262 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5625": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTTCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTTCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "465978", "accession": "APRA01000005.1", "fmin": "465153", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii NIPH 67", "NCBI_taxonomy_id": "1217627", "NCBI_taxonomy_cvterm_id": "42793"}, "protein_sequence": {"accession": "ENW50687.1", "sequence": "MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGSLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-262", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38118", "model_name": "OXA-262", "model_type_id": "40292"}, "3428": {"model_id": "3428", "ARO_accession": "3001717", "model_param": {"blastp_bit_score": {"param_value": "555", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-261 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5624": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTATTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAATGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "267077", "accession": "APQV01000009.1", "fmin": "266252", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii NIPH 201", "NCBI_taxonomy_id": "1217630", "NCBI_taxonomy_cvterm_id": "42792"}, "protein_sequence": {"accession": "ENW35072.1", "sequence": "MNIKALLFITSAIFISACSPYIVTANPNHNASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-261", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38117", "model_name": "OXA-261", "model_type_id": "40292"}, "3540": {"model_id": "3540", "ARO_accession": "3003635", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5735": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACTAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTCAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTGGAATTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGTTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182171.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79293.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAELRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNSRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFGIEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLVDSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-478", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40245", "model_name": "OXA-478", "model_type_id": "40292"}, "3541": {"model_id": "3541", "ARO_accession": "3003636", "model_param": {"blastp_bit_score": {"param_value": "520", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5736": {"dna_sequence": {"partial": "0", "sequence": "ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATAAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA", "fmax": "810", "accession": "KR182172.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Brachyspira pilosicoli", "NCBI_taxonomy_id": "52584", "NCBI_taxonomy_cvterm_id": "36935"}, "protein_sequence": {"accession": "ALC79294.1", "sequence": "MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-479", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40246", "model_name": "OXA-479", "model_type_id": "40292"}, "3542": {"model_id": "3542", "ARO_accession": "3003637", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5737": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTATTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KR872296.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ALL53530.1", "sequence": "MNIKALLFITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-480", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40247", "model_name": "OXA-480", "model_type_id": "40292"}, "3543": {"model_id": "3543", "ARO_accession": "3003639", "model_param": {"blastp_bit_score": {"param_value": "545", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "Assigned by Lahey's list of beta-lactamases, no accessions or other information available", "model_sequences": {"sequence": {"5738": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTAATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA", "fmax": "898", "accession": "KP264124.1", "fmin": "76", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AKF41839.1", "sequence": "MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVINQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-482", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40249", "model_name": "OXA-482", "model_type_id": "40292"}, "3423": {"model_id": "3423", "ARO_accession": "3001477", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-185 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5618": {"dna_sequence": {"partial": "0", "sequence": "TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA", "fmax": "747", "accession": "JQ396379.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Campylobacter jejuni", "NCBI_taxonomy_id": "197", "NCBI_taxonomy_cvterm_id": "36772"}, "protein_sequence": {"accession": "AFO09969.1", "sequence": "MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNIKIREELLEKYIYSLN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-185", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37877", "model_name": "OXA-185", "model_type_id": "40292"}, "3422": {"model_id": "3422", "ARO_accession": "3001463", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-158 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5617": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGACACTCTCTCGCTGGCGGCGCGGCGCGCTCGCGCTGCGCCTCCTCGGTGCGCTGGCCTCGCCCGTGGTCTTCGCAATGCCCGGACACGCCGCCGAACCCGCGCATTCTTCCGCGGTGCGCATCGCCGAGCGGGCCGACTGGGGCAAGTACTTTGCCGACGAAGGCGTCAAGGGCACGGTCATCGTGCTGGACGGCCGGACCCAGACCTATCAGGCTTACGATGCCGCACGCGCCGAGCGCCGCATGTCGCCCGCATCGACCTACAAGATATTCAACAGCCTGCTCGCGCTGGAGTCCGGCGCGCTCGACAACGAGCGCGAGGTCATCCCGTGGGACGGCAAGCCGCGTCGCGTCAAGGCGTGGAACGCCGCGCTCGATCTGCGCAACGCGTTTCGCGTGTCGTGCCTGCCTTGCTATCAGGTCGTCTCGCACAAGATCCCGCGCCAGTACGCGCAGGCCAAGCTCAACGAGGCGGGCTACGGCAATCGCACGATCGGCCGCGCCGCGCACGCCTACTGGATCGACGACAGCCTGCAGATTTCGGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCCACGGGCACGCTGCCGTTCTCGGCGCGCTCGCAGGACATCGTGCGCAACATATCGATCGTCGAAGCGAACGTCGACTACGTGCTGCACGGCAAGACGGGCTGGTTTACCGAAAAGAAACCCGACATCGGGTGGTGGGTCGGCTGGCTCGAGCGTGACGGCAACCTCACCATGATCGCGTTGAACATCGACATTCAAACCGATGCCGACGCGCCAAAGCGCGCGCGCATCGTTCGCAACGTGCTCAAGGATCTGAAGCTGATCTGA", "fmax": "1880", "accession": "KP771986.1", "fmin": "1028", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea sp. Va8523", "NCBI_taxonomy_id": "1705920", "NCBI_taxonomy_cvterm_id": "42789"}, "protein_sequence": {"accession": "ALA99192.1", "sequence": "MKKTLSRWRRGALALRLLGALASPVVFAMPGHAAEPAHSSAVRIAERADWGKYFADEGVKGTVIVLDGRTQTYQAYDAARAERRMSPASTYKIFNSLLALESGALDNEREVIPWDGKPRRVKAWNAALDLRNAFRVSCLPCYQVVSHKIPRQYAQAKLNEAGYGNRTIGRAAHAYWIDDSLQISAREQVDFLQRLATGTLPFSARSQDIVRNISIVEANVDYVLHGKTGWFTEKKPDIGWWVGWLERDGNLTMIALNIDIQTDADAPKRARIVRNVLKDLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-158", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37863", "model_name": "OXA-158", "model_type_id": "40292"}, "3421": {"model_id": "3421", "ARO_accession": "3001462", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-157 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5616": {"dna_sequence": {"partial": "0", "sequence": "ATGATGATGCTTTCTCGCTGGCGTCGTAGCGCCGTTGTGCTGCGAATCGCCGCTGCACTGTTATCCCCGTTGGCGGTTGCGATACCGGCGCATGCGGACGCTATTGCCAATGCCGCTAATGCCGTAGCGCCGAAAATCGTGGAGCGGGCCGACTGGGGCAAGTACTTCGACGCCGAAGGCGCGAAGGGCACGATCATCGTGCTCGACGGCCGCACCGGGGGCTATCAGGCCTATGACAGCACTCGCGCGAATCAGCGCATGTCGCCAGCTTCAACGTACAAGATATTCAACAGTTTGCTGGCGCTGGAGTCTGGCGCACTCGACAACGAGCGCGAAATCATTCCTTGGGATGGCAAGCCACGTAGCATGAAGCGCTGGAACGCAGCAATGAATCTGCGCGATGCGTTCCGGGTGTCGTGTCTGCCGTGCTATCAGGTTGTGTCGCGCAAGATTGCGCGGACCTATGCGCAGGGCAAGCTCGATGCGGTGGGCTATGGCAATCACACCATCGGGTCCGCAGCGGATGCGTATTGGGTCGACAACAGCCTGCAAATTTCAGCGCGTGAGCAGGTGGTGTTTCTGCAACGGCTGGCGCGCGGGCAGTTGCCGTTCTCGGCGCGCACGCAGGACATCGTGCGGCAGATTTCGATTGCCGAAGCGAACATGGACTACGTCCTGCACGGCAAGACCGGCTGGTATGTCGATGGCAAGCACGACATTGGCTGGTGGGTCGGTTGGATCGAACGGGACGGCAATATCACCACGGTTGCGCTGAACATGGACATGCGCAGCGACGCCGACGCGCCCAAGCGTGCCCGGATTGCCCGTGCGGTGTTGAAGGATCTGAAGTTGATCTGA", "fmax": "1030", "accession": "KP771985.1", "fmin": "172", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea norimbergensis", "NCBI_taxonomy_id": "93219", "NCBI_taxonomy_cvterm_id": "42788"}, "protein_sequence": {"accession": "ALA99191.1", "sequence": "MMMLSRWRRSAVVLRIAAALLSPLAVAIPAHADAIANAANAVAPKIVERADWGKYFDAEGAKGTIIVLDGRTGGYQAYDSTRANQRMSPASTYKIFNSLLALESGALDNEREIIPWDGKPRSMKRWNAAMNLRDAFRVSCLPCYQVVSRKIARTYAQGKLDAVGYGNHTIGSAADAYWVDNSLQISAREQVVFLQRLARGQLPFSARTQDIVRQISIAEANMDYVLHGKTGWYVDGKHDIGWWVGWIERDGNITTVALNMDMRSDADAPKRARIARAVLKDLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-157", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37862", "model_name": "OXA-157", "model_type_id": "40292"}, "3420": {"model_id": "3420", "ARO_accession": "3001461", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-156 is a beta-lactamase. From the Lahey list of OXA beta-lactamases.", "model_sequences": {"sequence": {"5615": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGACATTCTCCCGCTGGCGGCGCGGCGCGCTCGTGTTGCGCATCCTTGGCGCGCTGGCCTCGCCCGTGGTCTTCGCAACGCCGGGGCATGCCGCCGAACCCGTGCGTCCCCCTTCCGTACATATCACCGAGCGGGCCGATTGGGGGAAGTACTTTGCTGATGAAGGCGTCAAAGGCACCGTCGTCGTGCTCGACGGCCGCACGCAGACCTATCAGGCGTACGACGCCGCGCGCGCCGAGCGGCGCCTGTCGCCGGCATCAACCTACAAGATTTTCAACAGCTTGCTGGCGCTCGAATCGGGGGCGATCGACAACGAACGCGAAGTCATTCCCTGGGACGGCAAGCCGCGTAGCATGAAGGCGTGGAACGCGGCGCTCAACCTGCGGGACGCGTTCCGCGTGTCATGTCTGCCTTGCTATCAGATCCTCTCGCACAAGATCCCGCGTCAGTATGCGCAGGCCAAACTCAACGAGGTGGGCTATGGCAATCGCACGATCGGCCACGCCGCGGACACCTATTGGGTCGACGACAGCCTGCAGATTTCGGCGCGCGAACAGGTCGACTTCCTGCAGCGTTTGGCGAAGGGCACGCTGCCGTTCTCGGCGCGCTCGCAGGACATCGTGCGGAACATCTCGATCGTGGAAGCGAATGCCGACTACGTGCTGCACGGCAAGACGGGCTGGTTCACCGACAAGAAGCCCGACATCGGCTGGTGGGTGGGTTGGCTCGAGCGTGACGGCAACCTCACCATGATCGCCCTGAACATCGATATACAGTCGGATGCCGACGGGCCGAAGCGCGTGCGCATCGTCCGAAGCGTGCTCAAGGATCTGAAGTTGATCTGA", "fmax": "4175342", "accession": "UGSJ01000001.1", "fmin": "4174490", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea pulmonicola", "NCBI_taxonomy_id": "93221", "NCBI_taxonomy_cvterm_id": "42787"}, "protein_sequence": {"accession": "SUA92210.1", "sequence": "MKKTFSRWRRGALVLRILGALASPVVFATPGHAAEPVRPPSVHITERADWGKYFADEGVKGTVVVLDGRTQTYQAYDAARAERRLSPASTYKIFNSLLALESGAIDNEREVIPWDGKPRSMKAWNAALNLRDAFRVSCLPCYQILSHKIPRQYAQAKLNEVGYGNRTIGHAADTYWVDDSLQISAREQVDFLQRLAKGTLPFSARSQDIVRNISIVEANADYVLHGKTGWFTDKKPDIGWWVGWLERDGNLTMIALNIDIQSDADGPKRVRIVRSVLKDLKLI"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-156", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37861", "model_name": "OXA-156", "model_type_id": "40292"}, "3427": {"model_id": "3427", "ARO_accession": "3001716", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-260 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5622": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACACTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "342561", "accession": "APOR01000009.1", "fmin": "341736", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii NIPH 1362", "NCBI_taxonomy_id": "1217642", "NCBI_taxonomy_cvterm_id": "42791"}, "protein_sequence": {"accession": "ENU54757.1", "sequence": "MNIKAHLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-260", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38116", "model_name": "OXA-260", "model_type_id": "40292"}, "3426": {"model_id": "3426", "ARO_accession": "3001715", "model_param": {"blastp_bit_score": {"param_value": "540", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-259 is a beta-lactamase found in Acinetobacter spp.", "model_sequences": {"sequence": {"5621": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "KF305666.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "AGV04655.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-259", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38115", "model_name": "OXA-259", "model_type_id": "40292"}, "3425": {"model_id": "3425", "ARO_accession": "3001501", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-252 is a beta-lactamase found in Shewanella spp.", "model_sequences": {"sequence": {"5620": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGCGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTGGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG", "fmax": "2725083", "accession": "CP022089.2", "fmin": "2724285", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Shewanella sp. FDAARGOS_354", "NCBI_taxonomy_id": "1930557", "NCBI_taxonomy_cvterm_id": "42790"}, "protein_sequence": {"accession": "ASF15667.1", "sequence": "MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVALWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-252", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37901", "model_name": "OXA-252", "model_type_id": "40292"}, "3424": {"model_id": "3424", "ARO_accession": "3001496", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. 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 a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "OXA-234 is a beta-lactamase found in Acinetobacter baumannii", "model_sequences": {"sequence": {"5619": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "925", "accession": "NG_050607.1", "fmin": "100", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "WP_038350216.1", "sequence": "MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin 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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36026": {"category_aro_name": "OXA beta-lactamase", "category_aro_cvterm_id": "36026", "category_aro_accession": "3000017", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime."}}, "ARO_name": "OXA-234", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37896", "model_name": "OXA-234", "model_type_id": "40292"}}}