{"$update": {"2713": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2711": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2907": {"$update": {"ARO_category": {"$insert": {"37021": {"category_aro_name": "virginiamycin S2", "category_aro_cvterm_id": "37021", "category_aro_accession": "3000677", "category_aro_class_name": "Antibiotic", "category_aro_description": "Virginiamycin S2 is a streptogramin B antibiotic."}, "35945": {"category_aro_name": "streptogramin antibiotic", "category_aro_cvterm_id": "35945", "category_aro_accession": "0000026", "category_aro_class_name": "Drug Class", "category_aro_description": "Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30."}, "35964": {"category_aro_name": "lincomycin", "category_aro_cvterm_id": "35964", "category_aro_accession": "0000046", "category_aro_class_name": "Antibiotic", "category_aro_description": "Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction."}, "35936": {"category_aro_name": "lincosamide antibiotic", "category_aro_cvterm_id": "35936", "category_aro_accession": "0000017", "category_aro_class_name": "Drug Class", "category_aro_description": "Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides."}}}}}, "154": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2732": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2904": {"$update": {"ARO_description": "PoxtA is an ABC-F subfamily ATP-binding cassette protein that confers resistance to tetracycline, -phenicol, and oxazolidinone via modification of the bacterial ribosome. The encoding gene was isolated from a methicillin-resistant Staphylococcus aureus strain."}}, "334": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1344": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2775": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1786": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "_version": "3.0.2", "215": {"$update": {"ARO_description": "The bcrC gene product (BcrC) is an undecaprenyl pyrophosphate phosphatase originally isolated from Bacillus subtilis. When overexpressed it can confer resistance to bacitracin."}}, "276": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "1213": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "84": {"$update": {"ARO_category": {"$update": {"39772": {"$update": {"category_aro_description": "GIM beta-lactamase enzymes isolated from Pseudomonas aeruginosa, and found to confer broad-spectrum resistance to beta-lactam antibiotics."}}}}}}, "1256": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2321": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2207": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1191": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "45": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2223": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s).", "ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "957": {"$update": {"ARO_description": "TetG is a tetracycline efflux protein found in Gram-negative bacteria. The encoding gene is found in both chromosomal and plasmid DNA where it is frequently linked to the floR, sul1, and cmlA9 genes which encode proteins that can confer florfenicol/chloramphenicol, sulfamethoxazole, and chloramphenicol resistance, respectively."}}, "2306": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "182": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1305": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1442": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2063": {"$update": {"ARO_category": {"$update": {"41361": {"$update": {"category_aro_description": "blaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aureus."}}}}}}, "2263": {"$update": {"ARO_description": "OptrA is a member of the ABC-F protein subfamily that confers resistance to oxazolidinones. The gene encoding the protein was originally isolated from a plasmid in Enterococcus faecalis and Enterococcus faecium."}}, "2112": {"$update": {"model_sequences": {"$update": {"sequence": {"5129": {"dna_sequence": {"partial": "0", "sequence": "ATGAAGACAGTTCAATTTTTTTGGCATTATTTTAAGGTCTACAAGTTCTCATTTGTAGTTGTCATCCTGATGATTGTTCTGGCGACTTTTGCCCAAGCCCTCTTTCCAGTCTTTTCTGGACAAGCGGTGACGCAGCTAGCCAATTTAGTTCAAGCTTATCAAAATGGCAATCCAGAACTTGTATGGCAAAGCCTATCAGGAATCATGGTCAATCTTGGCCTGCTGGTTTTGGTTCTATTTATCTCTAGTGTAATATACATGTGTCTCATGACGCGCGTGATTGCAGAATCGACCAACGAGATGCGCAAAGGCCTCTTTGGTAAGCTTGCTCAGTTGACGGTTTCTTTCTTTGACCGTCGACAAGATGGCGATATCCTGTCTCATTTTACCAGTGATTTGGATAATATCCTCCAAGCCTTTAACGAAAGCTTGATTCAGGTCATGAGCAATATTGTTTTATACATTGGTCTGATTCTTGTCATGTTTTCGAGAAATGTGACGCTGGCTCTCATCACCATTGCCAGCACCCCATTGGCTTTCCTTATGCTGATTTTCATCGTGAAAATGGCACGCAAATACACCAACCTCCAGCAGAAAGAGGTAGGGAAGCTCAACGCCTATATGGATGAGAGCATCTCAGGCCAAAAAGCCGTGATTGTGCAAGGAATTCAAGAGGATATGATGGCAGGATTTCTTGAACAAAATGAGCGCGTGCGCAAGGCAACCTTTAAAGGAAGAATGTTCTCAGGAATTCTTTTCCCTGTCATGAATGGGATGAGCCTGATTAATACAGCCATCGTCATCTTTGCTGGTTCGGCTGTACTTTTGAATGATAAGTCTATTGAAACAAGTACAGCCCTAGGTTTGATTGTTATGTTTGCACAATTTTCACAGCAGTACTACCAGCCTATTATCCAAGTTGCAGCGAGTTGGGGAAGCCTTCAGTTGGCCTTTACTGGAGCTGAACGAATTCAGGAAATGTTTGATGCAGAGGAGGAAATCCGACCTGAAAAGGCTCCAACCTTCACTAAGTTGCAAGAAAGTGTTGAAATCAGTCATATCGTTTTTTCATACTTGCCTGATAAACCTATTTTGAAAGATGTCAGCATTTCTGCCCCTAAAGGCCAGATGACAGCAGTTGTTGGGCCGACAGGTTCAGGAAAAACGACTATTATGAACCTCATCAATCGCTTTTATGATGTTGATGCTGGTGGTATTTATTTTGATGGTAAAGACATTCGTGGCTATGACTTAGATAGTCTTAGAAGCAAGGTGGGAATTGTATTGCAAGATTCGGTCTTGTTTAGCGGAACGATTAGAGACAATATCCGATTTGGTGTGCCAGATGCTAGTCAGGAAATGGTTGAGGTAGCAGCAAAAGCAACCCACATTCACGACTATATCGAAAGTTTGCCTGATAAGTACGATACTCTTATTGATGATGACCAGAGCATCTTTTCAACAGGGCAGAAGCAATTGATTTCAATCGCTCGAACCCTGATGACAGATCCAGAAGTTCTCATTCTCGATGAAGCAACTTCAAACGTAGATACGGTGACAGAAAGCAAGATTCAGCATGCCATGGAGGTGGTTGTAGCAGGTAGAACTAGTTTCGTCATTGCCCACCGCTTGAAAACCATTCTCAATGCAGATCAGATTATTGTCCTTAAAGATGGAGAAGTCATTGAACGTGGTAACCACCATGAACTTTTGAAGCTAGGTGGCTTTTATTCAGAACTCTATCACAATCAATTTGTTTTCGAATAA", "fmax": "1982324", "accession": "AE005672.3", "fmin": "1980557", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Streptococcus pneumoniae TIGR4", "NCBI_taxonomy_id": "170187", "NCBI_taxonomy_cvterm_id": "40078"}, "protein_sequence": {"accession": "AAK76136.1", "sequence": "MKTVQFFWHYFKVYKFSFVVVILMIVLATFAQALFPVFSGQAVTQLANLVQAYQNGNPELVWQSLSGIMVNLGLLVLVLFISSVIYMCLMTRVIAESTNEMRKGLFGKLAQLTVSFFDRRQDGDILSHFTSDLDNILQAFNESLIQVMSNIVLYIGLILVMFSRNVTLALITIASTPLAFLMLIFIVKMARKYTNLQQKEVGKLNAYMDESISGQKAVIVQGIQEDMMAGFLEQNERVRKATFKGRMFSGILFPVMNGMSLINTAIVIFAGSAVLLNDKSIETSTALGLIVMFAQFSQQYYQPIIQVAASWGSLQLAFTGAERIQEMFDAEEEIRPEKAPTFTKLQESVEISHIVFSYLPDKPILKDVSISAPKGQMTAVVGPTGSGKTTIMNLINRFYDVDAGGIYFDGKDIRGYDLDSLRSKVGIVLQDSVLFSGTIRDNIRFGVPDASQEMVEVAAKATHIHDYIESLPDKYDTLIDDDQSIFSTGQKQLISIARTLMTDPEVLILDEATSNVDTVTESKIQHAMEVVVAGRTSFVIAHRLKTILNADQIIVLKDGEVIERGNHHELLKLGGFYSELYHNQFVFE"}}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "750"}}}}}}, "1670": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "2211": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1374": {"$update": {"ARO_category": {"$update": {"41361": {"$update": {"category_aro_description": "blaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aureus."}}}}}}, "995": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2550": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"$insert": {"8663": "C245T", "8664": "D71V", "8665": "T82I", "8666": "T82V", "8667": "A118T"}}, "clinical": {"$insert": {"8663": "C245T", "8664": "D71V", "8665": "T82I", "8666": "T82V", "8667": "A118T"}}}}}}}}, "1139": {"$update": {"model_sequences": {"$update": {"sequence": {"5110": {"dna_sequence": {"partial": "0", "sequence": "ATGAACTCGGAATCAGTACGCATTTATCTCGTTGCTGCGATGGGAGCCAATCGGGTTATTGGCAATGGTCCTAATATCCCCTGGAAAATTCCGGGTGAGCAGAAGATTTTTCGCAGACTCACTGAGGGAAAAGTCGTTGTCATGGGGCGAAAGACCTTTGAGTCTATCGGCAAGCCTCTACCGAACCGTCACACATTGGTAATCTCACGCCAAGCTAACTACCGCGCCACTGGCTGCGTAGTTGTTTCAACGCTGTCGCACGCTATCGCTTTGGCATCCGAACTCGGCAATGAACTCTACGTCGCGGGCGGAGCTGAGATATACACTCTGGCACTACCTCACGCCCACGGCGTGTTTCTATCTGAGGTACATCAAACCTTCGAGGGTGACGCCTTCTTCCCAATGCTCAACGAAACAGAATTCGAGCTTGTCTCAACCGAAACCATTCAAGCTGTAATTCCGTACACCCACTCCGTTTATGCGCGTCGAAACGGCTAA", "fmax": "22103", "accession": "GU585907.1", "fmin": "21605", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "ADG84870.1", "sequence": "MNSESVRIYLVAAMGANRVIGNGPNIPWKIPGEQKIFRRLTEGKVVVMGRKTFESIGKPLPNRHTLVISRQANYRATGCVVVSTLSHAIALASELGNELYVAGGAEIYTLALPHAHGVFLSEVHQTFEGDAFFPMLNETEFELVSTETIQAVIPYTHSVYARRNG"}}}}}}}, "1138": {"$update": {"model_sequences": {"$update": {"sequence": {"5131": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAACCCGCTGTCATCGCGCTGGTGATTACACTGCTGGACGCGATGGGAATTGGTCTGATCATGCCGGTATTACCGTCACTGCTGCGGGAATATCTCCCGGAAGCGGATGTGGCAAACCATTACGGCATTCTGCTGGCGCTGTATGCGGTGATGCAGGTCTGTTTTGCTCCGCTGCTGGGCAGATGGTCAGATAAGCTGGGGCGCAGACCGGTGCTGCTGTTATCCCTGGCGGGTGCCGCGTTTGATTACACACTGCTGGCACTGTCCAATGTGCTGTGGATGTTGTATCTCGGGCGGATTATCTCCGGGATCACTGGTGCCACCGGCGCGGTTGCGGCTTCGGTAGTGGCGGACAGCACGGCGGTCAGCGAGCGTACCGCCTGGTTCGGCCGTCTCGGTGCGGCCTTTGGTGCCGGGCTGATTGCCGGGCCGGCTATCGGCGGACTGGCGGGGGATATCTCACCGCATCTGCCGTTTGTCATTGCGGCAATACTGAATGCCTGCACCTTTCTGATGGTCTTTTTTATCTTTAAACCGGCGGTACAGACAGAAGAAAAACCGGCGGAGCAGAAACAAGAAAGCGCAGGTATCAGCTTTATCACACTGCTTAAACCTCTGGCGCTGTTGCTGTTTGTCTTTTTTACCGCGCAGCTTATCGGGCAGATCCCGGCCACTGTCTGGGTATTGTTTACGGAGAGCCGCTTTGCCTGGGACAGCGCGGCGGTCGGTTTTTCACTGGCGGGACTCGGGGCGATGCATGCACTGTTTCAGGCGGTGGTTGCCGGGGCGCTGGCAAAACGGCTGAGTGAGAAAACCATTATTTTCGCCGGATTTATTGCCGATGCCACCGCGTTTTTACTGATGTCTGCTATCACTTCCGGATGGATGGTGTATCCGGTCCTGATCCTGCTGGCAGGCGGCGGAATTGCACTGCCTGCATTGCAGGGCATTATCTCTGCCGGGGCATCGGCGGCAAATCAGGGAAAACTACAGGGTGTGCTGGTCAGCCTGACCAATCTGACCGGCGTGGCGGGCCCGCTGCTGTTTGCTTTTATTTTCAGTCAGACACAGCAGAGTGCGGACGGTACGGTGTGGCTGATTGGCACGGCACTGTACGGTCTGCTGCTGGCAATCTGTCTGCTGATCAGAAAACCGGCACCGGTGGCGGCCACCTGCTGA", "fmax": "1348", "accession": "AF467077.1", "fmin": "163", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Shigella flexneri Y", "NCBI_taxonomy_id": "424720", "NCBI_taxonomy_cvterm_id": "42476"}, "protein_sequence": {"accession": "AAL75563.1", "sequence": "MNKPAVIALVITLLDAMGIGLIMPVLPSLLREYLPEADVANHYGILLALYAVMQVCFAPLLGRWSDKLGRRPVLLLSLAGAAFDYTLLALSNVLWMLYLGRIISGITGATGAVAASVVADSTAVSERTAWFGRLGAAFGAGLIAGPAIGGLAGDISPHLPFVIAAILNACTFLMVFFIFKPAVQTEEKPAEQKQESAGISFITLLKPLALLLFVFFTAQLIGQIPATVWVLFTESRFAWDSAAVGFSLAGLGAMHALFQAVVAGALAKRLSEKTIIFAGFIADATAFLLMSAITSGWMVYPVLILLAGGGIALPALQGIISAGASAANQGKLQGVLVSLTNLTGVAGPLLFAFIFSQTQQSADGTVWLIGTALYGLLLAICLLIRKPAPVAATC"}}}}}}}, "2874": {"$update": {"ARO_category": {"$insert": {"40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}, "35971": {"category_aro_name": "penicillin", "category_aro_cvterm_id": "35971", "category_aro_accession": "0000054", "category_aro_class_name": "Antibiotic", "category_aro_description": "Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "40523": {"category_aro_name": "ticarcillin", "category_aro_cvterm_id": "40523", "category_aro_accession": "3003832", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death."}}}}}, "2769": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "442": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2761": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2760": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2425": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "618": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1623": {"$update": {"ARO_category": {"$update": {"39772": {"$update": {"category_aro_description": "GIM beta-lactamase enzymes isolated from Pseudomonas aeruginosa, and found to confer broad-spectrum resistance to beta-lactam antibiotics."}}}}}}, "_timestamp": "2019-04-25T18:52:07+00:00", "1647": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "3076": {"$update": {"model_sequences": {"$update": {"sequence": {"$update": {"4934": {"$update": {"dna_sequence": {"$update": {"partial": "0"}}}}}}}}}}, "2691": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "1005": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "2081": {"$update": {"model_sequences": {"$update": {"sequence": {"5128": {"dna_sequence": {"partial": "0", "sequence": "ATGCTGATTCAGAAAATAAAAACCTACAAGTGGCAGGCCCTGGCTTCGCTCCTGATGACAGGCTTGATGGTTGCTAGTTCACTTCTGCAACCGCGTTATCTGCAGGAAGTCTTAGGCGCCCTCCTTACTGGGAAATATGAAGCTATTTATAGTATCGGGGCTTGGTTGATTGGTGTGGCCGTAGTCGGTCTAGTTGCTGGTGGACTCAATGTTGTCCTCGCAGCCTATATTGCCCAAGGAGTTTCATCCGACCTTCGGGAGGATGCCTTCCGTAAAATTCAAACCTTTTCTTATGCTGATATTGAACAATTTAATGCGGGAAATCTAGTCGTTCGAATGACAAATGATATCAACCAGATTCAGAACGTTGTCATGATGACCTTCCAAATTCTTTTCAGACTTCCCCTCTTGTTCATCGGTTCGTTTATCCTAGCGGTTCAAACCTTACCTTCTCTGTGGTGGGTGATTGTTCTCATGGTAGTCTTGATTTTTGGTTTGACTGCTGTCATGATGGGAATGATGGGGCCTCGTTTTGCCAAGTTTCAAACCCTTCTTGAGCGCATCAATGCCATTGCCAAGGAAAATTTACGTGGCGTTCGTGTGGTCAAGTCCTTTGTCCAAGAAAAAGAGCAATTTGCTAAGTTTACAGAGGTCTCAGACGAGCTTCTTGGTCAAAACCTTTACATTGGTTATGCCTTTTCAGTAGTGGAACCCTTTATGATGTTGGTTGGTTACGGGGCGGTCTTCCTCTCTATTTGGCTGGTCGCGGGAATGGTTCAGTCGGATCCGTCTGTTGTTGGTTCCATCGCTTCTTTTGTTAATTACCTAAGCCAGATTATCTTTACCATTGTTATGGTTGGATTTTTGGGAAATTCTGTCAGCCGTGCCATGATTTCCATGCGTCGTATTCGAGAAATTCTTGACGCAGAGCCAGCTATGACCTTCAAGGATATCCCAGATGAAGAGTTGGTTGGAAGTCTTAGCTTTGAAAATGTGACCTTTACCTATCCAATGGACAAGGAACCGATGCTGAAAGATGTGAGCTTTACTATTGAACCTGGTCAAATGGTTGGTGTAGTTGGAGCGACTGGTGCAGGAAAGTCAACCTTGGCTCAATTGATTCCACGTCTCTTTGATCCACAGGACGGGGCCATTAAAATCGGTGGCAAGGATATTCGAGAAGTGAGTGAAGGAACCCTGCGTAAAACAGTTTCCATCGTTCTCCAACGTGCCATTCTTTTTAGTGGAACGATTGCAGATAACTTGAGACAGGGGAAGGGGAATGCTACTCTATTTGAAATGGAGCGCGCAGCCAATATTGCCCAGGCTAGTGAATTCATTCATCGTATGGAGAAAACCTTTGAAAGTCCAGTTGAAGAACGGGGAACCAATTTCTCTGGTGGACAAAAACAAAGGATGTCGATTGCGCGTGGGATTGTCAGCAATCCACGTATTCTGATTTTTGATGATTCGACCTCAGCCTTGGATGCCAAATCAGAGCGCTTGGTGCAAGAAGCTTTGAATAAGGACTTGAAGGGGACGACAACCATTATTATTGCTCAAAAAATTAGCTCGGTTGTCCATGCAGACAAGATCTTGGTTCTAAATCAAGGACGATTGATTGGTCAAGGTACGCATGCAGACTTGGTTGCCAACAATGCCGTTTACCGTGAAATCTATGAAACACAGAAATGA", "fmax": "1984810", "accession": "AE005672.3", "fmin": "1983115", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Streptococcus pneumoniae TIGR4", "NCBI_taxonomy_id": "170187", "NCBI_taxonomy_cvterm_id": "40078"}, "protein_sequence": {"accession": "AAK76137.1", "sequence": "MLIQKIKTYKWQALASLLMTGLMVASSLLQPRYLQEVLGALLTGKYEAIYSIGAWLIGVAVVGLVAGGLNVVLAAYIAQGVSSDLREDAFRKIQTFSYADIEQFNAGNLVVRMTNDINQIQNVVMMTFQILFRLPLLFIGSFILAVQTLPSLWWVIVLMVVLIFGLTAVMMGMMGPRFAKFQTLLERINAIAKENLRGVRVVKSFVQEKEQFAKFTEVSDELLGQNLYIGYAFSVVEPFMMLVGYGAVFLSIWLVAGMVQSDPSVVGSIASFVNYLSQIIFTIVMVGFLGNSVSRAMISMRRIREILDAEPAMTFKDIPDEELVGSLSFENVTFTYPMDKEPMLKDVSFTIEPGQMVGVVGATGAGKSTLAQLIPRLFDPQDGAIKIGGKDIREVSEGTLRKTVSIVLQRAILFSGTIADNLRQGKGNATLFEMERAANIAQASEFIHRMEKTFESPVEERGTNFSGGQKQRMSIARGIVSNPRILIFDDSTSALDAKSERLVQEALNKDLKGTTTIIIAQKISSVVHADKILVLNQGRLIGQGTHADLVANNAVYREIYETQK"}}}}}, "model_param": {"$update": {"blastp_bit_score": {"$update": {"param_value": "750"}}}}}}, "2213": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2212": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1041": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "1992": {"$update": {"ARO_description": "dfrA1 is an integron-encoded dihydrofolate reductase", "model_sequences": {"$update": {"sequence": {"5109": {"dna_sequence": {"partial": "0", "sequence": "GTGAAACTATCACTAATGGTAGCTATATCGAAGAATGGAGTTATCGGGAATGGCCCTGATATTCCATGGAGTGCCAAAGGTGAACAGCTCCTGTTTAAAGCTATTACCTATAACCAATGGCTGTTGGTTGGACGCAAGACTTTTGAATCAATGGGAGCATTACCCAACCGAAAGTATGCGGTCGTAACACGTTCAAGTTTTACATCTGACAATGAGAACGTAGTGATCTTTCCATCAATTAAAGATGCTTTAACCAACCTAAAGAAAATAACGGATCATGTCATTGTTTCAGGTGGTGGGGAGATATACAAAAGCCTGATCGATCAAGTAGATACACTACATATATCTACAATAGACATCGAGCCGGAAGGTGATGTTTACTTTCCTGAAATCCCCAGCAATTTTAGGCCAGTTTTTACCCAAGACTTCGCCTCTAACATAAATTATAGTTACCAAATCTGGCAAAAGGGTTAA", "fmax": "20000", "accession": "KJ541681.1", "fmin": "19526", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella oxytoca", "NCBI_taxonomy_id": "571", "NCBI_taxonomy_cvterm_id": "36788"}, "protein_sequence": {"accession": "AAP74961.2", "sequence": "MKLSLMVAISKNGVIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSSFTSDNENVVIFPSIKDALTNLKKITDHVIVSGGGEIYKSLIDQVDTLHISTIDIEPEGDVYFPEIPSNFRPVFTQDFASNINYSYQIWQKG"}}}}}}}, "1554": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1608": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "1975": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2056": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "1820": {"$update": {"ARO_description": "The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin."}}, "1971": {"$update": {"model_sequences": {"$update": {"sequence": {"5108": {"dna_sequence": {"partial": "0", "sequence": "ATGGGTCAAAGTAGCGATGAAGCCAACGCTCCCGTTGCAGGGCAGTTTGCGCTTCCCCTGAGTGCCACCTTTGGCTTAGGGGATCGCGTACGCAAGAAATCTGGTGCCGCTTGGCAGGGTCAAGTCGTCGGTTGGTATTGCACAAAACTCACTCCTGAAGGCTATGCGGTCGAGTCCGAATCCCACCCAGGCTCAGTGCAAATTTATCCTGTGGCTGCACTTGAACGTGTGGCCTAA", "fmax": "38255", "accession": "DQ839391.1", "fmin": "38018", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "ABI20482.1", "sequence": "MGQSSDEANAPVAGQFALPLSATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVAALERVA"}}}}}}}, "726": {"$update": {"ARO_category": {"$update": {"41361": {"$update": {"category_aro_description": "blaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aureus."}}}}}}, "2208": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2752": {"$update": {"model_sequences": {"$update": {"sequence": {"5122": {"dna_sequence": {"partial": "0", "sequence": "GTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTCTTGTTATGACATGTTTTTTTGGGGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA", "fmax": "1194", "accession": "X02340.1", "fmin": "222", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "CAA26199.1", "sequence": "MVTAQWRFSWLLVMTCFFGVQSMPRASKQQARYAVGRCLMLWSSNDVTQQGSRPKTKLNIMREAVIAEVSTQLSEVVGVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"}}}}}}}, "2066": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "1474": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "1386": {"$update": {"model_sequences": {"$update": {"sequence": {"5121": {"dna_sequence": {"partial": "0", "sequence": "ATGAGCAATTTGATTAACGGAAAAATACCAAATCAAGCGATTCAAACATTAAAAATCGTAAAAGATTTATTTGGAAGTTCAATAGTTGGAGTATATCTATTTGGTTCAGCAGTAAATGGTGGTTTACGCATTAACAGCGATGTAGATGTTCTAGTCGTCGTGAATCATAGTTTACCTCAATTAACTCGAAAAAAACTAACAGAAAGACTAATGACTATATCAGGAAAGATTGGAAATACGGATTCTGTTAGACCACTTGAAGTTACGGTTATAAATAGGAGTGAAGTTGTCCCTTGGCAATATCCTCCAAAAAGAGAATTTATATACGGTGAGTGGCTCAGGGGTGAATTTGAGAATGGACAAATTCAGGAACCAAGCTATGATCCTGATTTGGCTATTGTTTTAGCACAAGCAAGAAAGAATAGTATTTCTCTATTTGGTCCTGATTCTTCAAGTATACTTGTCTCCGTACCTTTGACAGATATTCGAAGAGCAATTAAGGATTCTTTGCCAGAACTAATTGAGGGGATAAAAGGTGATGAGCGTAATGTAATTTTAACCCTAGCTCGAATGTGGCAAACAGTGACTACTGGTGAAATTACCTCGAAAGATGTCGCTGCAGAATGGGCTATACCTCTTTTACCTAAAGAGCATGTAACTTTACTGGATATAGCTAGAAAAGGCTATCGGGGAGAGTGTGATGATAAGTGGGAAGGACTATATTCAAAGGTGAAAGCACTCGTTAAGTATATGAAAAATTCTATAGAAACTTCTCTCAATTAG", "fmax": "1113", "accession": "X02588.1", "fmin": "330", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus aureus", "NCBI_taxonomy_id": "1280", "NCBI_taxonomy_cvterm_id": "35508"}, "protein_sequence": {"accession": "CAA26428.1", "sequence": "MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN"}}}}}}}, "1390": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "2693": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}, "1368": {"$update": {"ARO_category": {"$update": {"35963": {"$update": {"category_aro_name": "acriflavine", "category_aro_description": "Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish."}}}}}}, "431": {"$update": {"model_description": "This model detects protein overexpression based on the presence of mutations. The detection of the protein without an associated mutation indicates that the protein is likely to be expressed at low or basal levels. The detection of the protein with the mutation indicates that the protein is likely overexpressed. This model reflects how certain proteins are functional with and without mutations. For example, efflux pump subunits and regulators are functional with mutations and without mutations. Without mutations, efflux pump subunits and regulators are usually expressed at a low level. When an efflux pump regulator has a mutation, it can cause the overexpression of the efflux pump it is responsible for regulating, leading to resistance to specific drugs. Protein overexpression models have two parameters: a curated BLASTP cutoff, and a curated set of mutations (single resistance variants, frameshift mutations, indels, etc.) shown clinically to confer resistance. This model type is a combination of the protein homolog and protein variant model. A detected hit can be categorized as Perfect, Strict, or Loose with no mutation(s) or as Strict or Loose with mutation(s)."}}}, "$delete": ["2325"], "$insert": {"3258": {"model_id": "3258", "ARO_accession": "3004550", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene from non-O1, non-O139 Vibrio cholerae", "model_sequences": {"sequence": {"5114": {"dna_sequence": {"partial": "0", "sequence": "GTGAAAATATCACTAATGGCTGCAAAAGCAAGAAATGGGGTTATTGGCTGCGGCTCGGATATCCCGTGGAACGCTAAAGGTGAGCAGCTGCTTTTTAAAGCAATAACTTACAATCAATGGCTCTTAGTCGGCCGTAAAACATTTGAGGCAATGGGGGCTCTCCCAAATAGAAAGTATGCAGTTGTCAGCCGCTCAGGATCGGTAGCTACTAACGATGATGTGGTTGTGTTTCCATCTATAGAAGCAGCAATGAGGGAGCTAAAGACTCTTACGAACCATGTTGTTGTTTCTGGTGGTGGAGAGATCTACAAGAGTCTGATCGCCCATGCCGACACGCTACATATCTCGACAATAGATTCCGAGCCAGAGGGCAATGTTTTCTTTCCGGAAATCCCCAAAGAGTTCAATGTGGTGTTCGAGCAGGAATTTCATTCAAATATAAATTATCGCTATCAAATCTGGCAAAGGGGTTAA", "fmax": "2821", "accession": "KP076293.1", "fmin": "2347", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio cholerae non-O1/non-O139", "NCBI_taxonomy_id": "156539", "NCBI_taxonomy_cvterm_id": "36920"}, "protein_sequence": {"accession": "ACD45689.1", "sequence": "MKISLMAAKARNGVIGCGSDIPWNAKGEQLLFKAITYNQWLLVGRKTFEAMGALPNRKYAVVSRSGSVATNDDVVVFPSIEAAMRELKTLTNHVVVSGGGEIYKSLIAHADTLHISTIDSEPEGNVFFPEIPKEFNVVFEQEFHSNINYRYQIWQRG"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA27", "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": "42453", "model_name": "dfrA27", "model_type_id": "40292"}, "3259": {"model_id": "3259", "ARO_accession": "3004551", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene from Aeromonas hydrophilia", "model_sequences": {"sequence": {"5115": {"dna_sequence": {"partial": "0", "sequence": "GTGAAAATATCACTAATGGCTGCAAAAGCAAGAAATGGGGTTATTGGCTGCGGCTCTGATATCCCTTGGAACGCTAAAGGCGAGCAGCTGCTTTTTAAAGCAATAACTTACAATCAGTGGCTTTTAGTCGGCCGCAAAACATTTGAGGCAATGGGGGCTCTCCCAAATAGAAAGTATGCAGTTGTCAGCCGCTCAGGATCGGTAGCTACTAACGATGATATGGTTGTGTTTCCATCTATAGAAGCAGCAATGGGTAAGCTAAAGACTCTTACGAACCATGTTGTTGTTTCTGGTGGTGGAGAGATCTATAAGAGTCTGATCGCCCATGCCGACACGCTACATATTTCGACAATAGATTCCGAGCCAGAGGGCAATGTTTTCTTTCCGGAAATCCCCAAAGATTTCAATGTGGTGTTCGAGCAGGAATTTCATTCAAATATAAATTATCGATATCAAATCTGGCAAAGGGGTTAA", "fmax": "589", "accession": "FM877476.1", "fmin": "115", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Aeromonas hydrophila", "NCBI_taxonomy_id": "644", "NCBI_taxonomy_cvterm_id": "36810"}, "protein_sequence": {"accession": "CAT00035.1", "sequence": "MKISLMAAKARNGVIGCGSDIPWNAKGEQLLFKAITYNQWLLVGRKTFEAMGALPNRKYAVVSRSGSVATNDDMVVFPSIEAAMGKLKTLTNHVVVSGGGEIYKSLIAHADTLHISTIDSEPEGNVFFPEIPKDFNVVFEQEFHSNINYRYQIWQRG"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA28", "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": "42454", "model_name": "dfrA28", "model_type_id": "40292"}, "3270": {"model_id": "3270", "ARO_accession": "3004568", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 trimethoprim-resistant dihydrofolate reductase identified from Vibrio cholerae", "model_sequences": {"sequence": {"5130": {"dna_sequence": {"partial": "0", "sequence": "CTATCGCTCATACGTCGTCGCGATAGTGAAACTGCCGTTTTCGATAATGTGGCCTCTGGACGTTACGCGCCATTGTCGGCCTTCAGTGTCGTATCCGGGACTTTCCCAGAATACGTCTACGTGAGTATCCGCTGCAGGATACGCCCTCAACACCTTCGTTTCAAAAACCTTCGTAATGACGTCTTTGTGCAGATTATAGATTTCAGCACCGCCCGCCACGATGATCTCAGTAACGCCCAGGTGTTCGGCCACTTCAAACAGATGGCAGCTATTCCCCCACGCTACAAAGGTGCCGTCTCCACGTTCGGTTATATCCGCTTTATCGTAAGGCTCGCGTGTGAGCACGATGACGTTGCGTCCGGGCAGGCCATTGGGGATGCTCTCAAAGGTCTTTCTGCCCATGACGAGTGTCTTACCCATAGTGATCGCTTTGAAGCGTTTGAGGTCTTCTTTCAACCGAACTCCTTCGACATGCCAAGGCAAGTCGCCGTCCTGACCAATCTCACCGTTTACACCACGCGCTACAATCATTGAAAATTGAATTTCTTTATTCAT", "fmax": "7967", "accession": "AY034138.1", "fmin": "7412", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio cholerae MO10", "NCBI_taxonomy_id": "345072", "NCBI_taxonomy_cvterm_id": "39556"}, "protein_sequence": {"accession": "AAK64581.1", "sequence": "MNKEIQFSMIVARGVNGEIGQDGDLPWHVEGVRLKEDLKRFKAITMGKTLVMGRKTFESIPNGLPGRNVIVLTREPYDKADITERGDGTFVAWGNSCHLFEVAEHLGVTEIIVAGGAEIYNLHKDVITKVFETKVLRAYPAADTHVDVFWESPGYDTEGRQWRVTSRGHIIENGSFTIATTYER"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA18", "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": "42475", "model_name": "dfrA18", "model_type_id": "40292"}, "3271": {"model_id": "3271", "ARO_accession": "3004569", "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": "A chromosomally-encoded colistin resistance phosphoethanolamine (PEtN) transferase of Moraxella osloensis. ICR-Mo represents the closest known ortholog to the colistin resistance MCR-1 and MCR-2 PEtN transferases", "model_sequences": {"sequence": {"5132": {"dna_sequence": {"partial": "0", "sequence": "TTGGTGCATTTAGATAAGGTGAGTAATCGTATGTCAGTGAATAACTCTCGATGGTTAGCATGGCGTCAGCAAGGTATTAATGCTTATGTGATGATGGGTATTGTCGCGCTATTTTTGACCCTAACCGCCAATATTACTTTCTTTGATAAAGCCACGGAAGTCTATCCGTTTGCCCAGCATATTGGGTTTATAGGCTCATTGCCGTTGGTGCTATTCGGTGTCATGCTACTGGTTATTGTGCTGCTCAGCTATCGTTACACCCTTAAAGCGGTATTGATTTTTTTGCTATTGACCGCGGCAGTCACGGCGTATTTTACTGATACTTATGGCACTGTCTATGATGTCAATATGCTACAAAACGCGCTACAAACCGATAAAGCAGAAAGCGCCGATTTGTTTAACGTCAATTTTATCTTACGCATTTTATTGCTTGGGGTATTGCCTAGTGTGTGGGTGGCGTGGCAAAAGGTCACATTTCCCCCCATCAAGCGCAGCATATTGCAGCGCGGCTTGACGTATTTGGTCAGCCTCGGTTTGGTAGTGTTACCGATTTTGGCAATGAGTAAAAATTACGCCAGTTTTTTCCGTGAACATAAACAGCTTCGTAGCTATACCAATCCTGCAACCCCTGTATATGCACTGGGTAAACTTGCCAGTATACAGCTCAAACAAGCACAAGCTCCCAAAACCCAAATCATGCATGCCACCGATGCGGTGCAGGTGAGTAATCCTACCACCCGTAAGCCAAAACTGGTGGTATTTGTAGTTGGAGAAACCGCGCGCGGCGACCATGTGCAGCTAAATGGGTATAACCGAACTACCTTCCCGCAGATGGCAGCGACGGCTGGGGTAACTAATTTTAACCAAGTCATCGCCTGCGGTACCTCAACCGCTTATTCGGTGCCTTGTATGTTTAGTTATGTCGGCATGAAAGACTACGATGTGGATACCGCCAACTACCAAGAAAACGTACTTGATACCTTACATCGCCTAAAGGTTAATATCTTGTGGCGTGATAACAACTCAAGCTCAAAAGGCGTCACTAATCGTTTGCCCGCGGCGGATTTTGTCGATTATAAAACTGCGCGCAACAATACGATGTGTAATACCAACCCCTATGGCGAGTGCCGCGATGTGGGTATGCTAGTAGGCTTAGATGACTACGTCAAACAACAAGCTAACCAAAATACGCTTAACCAGGATACCCTAATTGTGCTGCACCAAATGGGTAATCACGGACCTGCGTATTTTAAACGATATGATAAGCAATTTGAAAAATTCACCCCAGTCTGCCAAAGCAATGAACTTGCCAAATGCGACCCACAAAGCGTGATTAATGCCTTTGACAATGCGCTACTTGCCACCGATGACTTTTTGGCAAAAACGGTGAACTGGTTAGACAAATATGACAGCACCCACCAAGTAGCGATGCTGTATGTCAGTGACCACGGTGAAAGTCTGGGCGAAAACGGCATCTATTTACATGGTATGCCTTATAAAATCGCGCCTAAAGCGCAAAAACACGTCGCATCGATGTTTTGGGCAGGTAAACACTCAGGCATTCAAGCAGTGCCATCTAATACTGAGCTCACCCATGATGCCATTACCCCAACCTTGTTAAAACTGTTTGATGTGCGTGCGCAAACCGTACAAGGCAAACCTTTATTTATCAAGTAA", "fmax": "1703306", "accession": "NZ_CP014234.1", "fmin": "1701629", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Moraxella osloensis", "NCBI_taxonomy_id": "34062", "NCBI_taxonomy_cvterm_id": "42478"}, "protein_sequence": {"accession": "WP_082741435.1", "sequence": "MVHLDKVSNRMSVNNSRWLAWRQQGINAYVMMGIVALFLTLTANITFFDKATEVYPFAQHIGFIGSLPLVLFGVMLLVIVLLSYRYTLKAVLIFLLLTAAVTAYFTDTYGTVYDVNMLQNALQTDKAESADLFNVNFILRILLLGVLPSVWVAWQKVTFPPIKRSILQRGLTYLVSLGLVVLPILAMSKNYASFFREHKQLRSYTNPATPVYALGKLASIQLKQAQAPKTQIMHATDAVQVSNPTTRKPKLVVFVVGETARGDHVQLNGYNRTTFPQMAATAGVTNFNQVIACGTSTAYSVPCMFSYVGMKDYDVDTANYQENVLDTLHRLKVNILWRDNNSSSKGVTNRLPAADFVDYKTARNNTMCNTNPYGECRDVGMLVGLDDYVKQQANQNTLNQDTLIVLHQMGNHGPAYFKRYDKQFEKFTPVCQSNELAKCDPQSVINAFDNALLATDDFLAKTVNWLDKYDSTHQVAMLYVSDHGESLGENGIYLHGMPYKIAPKAQKHVASMFWAGKHSGIQAVPSNTELTHDAITPTLLKLFDVRAQTVQGKPLFIK"}}}}, "ARO_category": {"36192": {"category_aro_name": "peptide antibiotic", "category_aro_cvterm_id": "36192", "category_aro_accession": "3000053", "category_aro_class_name": "Drug Class", "category_aro_description": "Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "36968": {"category_aro_name": "colistin B", "category_aro_cvterm_id": "36968", "category_aro_accession": "3000624", "category_aro_class_name": "Antibiotic", "category_aro_description": "Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria."}, "41681": {"category_aro_name": "intrinsic colistin resistant phosphoethanolamine transferase", "category_aro_cvterm_id": "41681", "category_aro_accession": "3004465", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Chromosomally-encoded phosphoethanolamine (PEtN) transferases shown to confer resistance to polymyxin antibiotics, including colistin."}, "36966": {"category_aro_name": "colistin A", "category_aro_cvterm_id": "36966", "category_aro_accession": "3000622", "category_aro_class_name": "Antibiotic", "category_aro_description": "Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria."}}, "ARO_name": "ICR-Mo", "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": "42477", "model_name": "ICR-Mo", "model_type_id": "40292"}, "3254": {"model_id": "3254", "ARO_accession": "3002361", "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": "NDM-11 is a beta-lactamase. From the Lahey list of NDM beta-lactamases.", "model_sequences": {"sequence": {"5107": {"dna_sequence": {"partial": "0", "sequence": "ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGGTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA", "fmax": "813", "accession": "KP265939.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AJE61443.1", "sequence": "MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGVVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"}}}}, "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."}, "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."}, "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."}, "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."}, "36196": {"category_aro_name": "NDM beta-lactamase", "category_aro_cvterm_id": "36196", "category_aro_accession": "3000057", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins."}}, "ARO_name": "NDM-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": "38761", "model_name": "NDM-11", "model_type_id": "40292"}, "3255": {"model_id": "3255", "ARO_accession": "3004547", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and antibiotic resistance gene identified from an integron in Vibrio cholerae", "model_sequences": {"sequence": {"5111": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAATATCCATTATGGCAGCTGTTTCCGAGAATGGAGTAATTGGCTCTGGATTGGATATACCTTGGCATGTATATGGTGAGCAGCTCCTGTTCAAAGCTATGACTTACAATCATTGGCTTTTAGTCGGTCGTAAAACTTTCGACTCAATGGGTAAACTTCCGAATAGGAAATATGCTGTGGTTACTCGTACTGAAATGGTCTCGAATGATCCTGATGTTGTTTATTTCACAAGCGTTGAATCGGCATTAGCTTACTTAGACCACACGACAACACATGTCTTTGTTTCTGGTGGTGGTGAAATTTACAAAGCATTAATCGAACAAGCAGATGTTATCCATCTTTCAGTGATTCATAAGCACATCTCTGGCGACGTGTTTTTCCCTTCAGTTCCACAGAGTTTCAAGCAAACATTTGAGCAAAGTTTCAGTTCAAATATTGATTACACGTACCAAATTTGGACAAAGGGCTAA", "fmax": "802", "accession": "FJ905898.1", "fmin": "328", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio cholerae", "NCBI_taxonomy_id": "666", "NCBI_taxonomy_cvterm_id": "36789"}, "protein_sequence": {"accession": "ACY06082.1", "sequence": "MKISIMAAVSENGVIGSGLDIPWHVYGEQLLFKAMTYNHWLLVGRKTFDSMGKLPNRKYAVVTRTEMVSNDPDVVYFTSVESALAYLDHTTTHVFVSGGGEIYKALIEQADVIHLSVIHKHISGDVFFPSVPQSFKQTFEQSFSSNIDYTYQIWTKG"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA6", "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": "42450", "model_name": "dfrA6", "model_type_id": "40292"}, "3256": {"model_id": "3256", "ARO_accession": "3004548", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene identified from porcine isolates of Esherichia coli", "model_sequences": {"sequence": {"5112": {"dna_sequence": {"partial": "0", "sequence": "ATGGCTTCTCTAAACATGATTGTCGCTGTCAATAAGACAGGAGGTATCGGATTTGAAAATCAGATTCCGTGGCATGAACCAGAAGATTTAAAACACTTCAAAGCTGTTACAATGAACTCAGTTTTGATTATGGGTAGAAAAACTTTTGCCTCACTGCCTAAAGTGCTGCCCGGACGACTTCATGTGGTAGTCAGTAAAACAGTACCACCCACCCAGAACACTGATCAAGTTGTGTATGTAAGTACATACCAGATCGCAGTAAGAACTGCAAGCTTGTTGGTTGACAAACCAGAGTATTCTCAAATTTTTGTAATTGGTGGGAAGAGTGCGTACGAGAACTTAGCTGCCTACGTGGACAAACTCTACTTAACTAGAGTACAGCTCAACACACAACAAGACACTGAACTGGATTTATCCCTATTCAAGTCATGGAAACTCGTATCTGAGGTCCCGACCATTACTGAAAACAAAACAAAACTTATTTTCCAAATTTGGATTAACCCTAACCCTATTAGTGAGGAACCCACATGTTAG", "fmax": "1259", "accession": "X57730.1", "fmin": "725", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "CAA40897.1", "sequence": "MASLNMIVAVNKTGGIGFENQIPWHEPEDLKHFKAVTMNSVLIMGRKTFASLPKVLPGRLHVVVSKTVPPTQNTDQVVYVSTYQIAVRTASLLVDKPEYSQIFVIGGKSAYENLAAYVDKLYLTRVQLNTQQDTELDLSLFKSWKLVSEVPTITENKTKLIFQIWINPNPISEEPTC"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA9", "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": "42451", "model_name": "dfrA9", "model_type_id": "40292"}, "3257": {"model_id": "3257", "ARO_accession": "3004549", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene identified from an integron in Pseudomonas aeruginosa", "model_sequences": {"sequence": {"5113": {"dna_sequence": {"partial": "1", "sequence": "ATGGACCAAGGCAGAAGTGAAGTCAGTAATCCAGTTGCTGGCCAGTTTGCGTTCCCTTCAAACGCCGCGTTCGGAATGGGAGATCGCGTGCGCAAGAAATCTGGCGCCGCTTGGCAAGGCCAGATTGTCGGGTGGTACTGCACAAAATTGACCCCTGAAGGGTACGCTGTCGAGTCTGAGGCTCACCCTGGCTCGGTACAGATTTATCCTGTTGCGGCACTGGAACGCATCAACTGA", "fmax": "3092", "accession": "AY943084.1", "fmin": "2855", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AAX46054.1", "sequence": "MDQGRSEVSNPVAGQFAFPSNAAFGMGDRVRKKSGAAWQGQIVGWYCTKLTPEGYAVESEAHPGSVQIYPVAALERIN"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrB5", "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": "42452", "model_name": "dfrB5", "model_type_id": "40292"}, "3261": {"model_id": "3261", "ARO_accession": "3004553", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene", "model_sequences": {"sequence": {"5117": {"dna_sequence": {"partial": "0", "sequence": "ATGGACCAAGGCAGAAGTGAAGTCAGTAATCCAGTTGCTGGCCAGTTTGCGTTCCCTTCAAACGCCGCGTTCGGAATGGGAGATCGCGTGCGCAAGAAATCTGGCGCCGCTTGGCAAGGCCAGATTGTCGGGTGGTACTGCACAAAATTGACCCCTGAAGGGTACGCTGTCGAGTCTGAGGCTCACCCTGGCTCGGTACAGATTTATCCTGTTGCGGCACTGGAACGCATCAACTGA", "fmax": "404", "accession": "HE650984.1", "fmin": "167", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "bacterium AK-MB79", "NCBI_taxonomy_id": "1135898", "NCBI_taxonomy_cvterm_id": "42458"}, "protein_sequence": {"accession": "CCF70754.1", "sequence": "MDQGRSEVSNPVAGQFAFPSNAAFGMGDRVRKKSGAAWQGQIVGWYCTKLTPEGYAVESEAHPGSVQIYPVAALERIN"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfr-lie", "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": "42457", "model_name": "dfr-lie", "model_type_id": "40292"}, "3260": {"model_id": "3260", "ARO_accession": "3004552", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene from Klebsiella pneumoniae", "model_sequences": {"sequence": {"5116": {"dna_sequence": {"partial": "0", "sequence": "GTGAAAGTATCATTAATGGCTGCAAGAGCGAGAAACGGAGTGATCGGTTGCGGTCCACACATACCCTGGTCCGCGAAAGGAGAGCAGCTACTCTTTAAAGCCCTGACGTACAACCAGTGGCTTTTGGTTGGCCGCAAGACGTTCGAATCAATGGGGGCGCTCCCCAACAGGAAATACGCGGTCGTTACTCGCTCAGCCTGGACGGCCAATAATGACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCAACGGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCTACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATTCCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGTTAA", "fmax": "1178", "accession": "AM997279.2", "fmin": "704", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella sp. MB45", "NCBI_taxonomy_id": "871235", "NCBI_taxonomy_cvterm_id": "42456"}, "protein_sequence": {"accession": "CAQ53849.2", "sequence": "MKVSLMAARARNGVIGCGPHIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSAWTANNDNVVVFPSIEEAMGGLAKLNGHVIVSGGGEIYRETLPMASTLHVSTIDIEPEGDVFFPNIPNFFEVVFEQHFSSNINYCYQIWKKG"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA30", "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": "42455", "model_name": "dfrA30", "model_type_id": "40292"}, "3263": {"model_id": "3263", "ARO_accession": "3004555", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene identified from non-typhoidal multidrug-resistant Salmonella enterica", "model_sequences": {"sequence": {"5119": {"dna_sequence": {"partial": "0", "sequence": "TTGAAAATTTCATTGATTTCTGCAGTGTCAGAAAATGGCGTAATCGGTAGTGGTCCTGATATTCCGTGGTCAGCAAAAGGTGAGCAGCTAATCTTTAAGGCGCTCACATACAATCAGTGGCTTCTTGTTGGAAGGAAAACATTTGACTCTATGGGAGTTCTTCCAAATCGCAAATATGCAGTAGTGTCAAAGAATGGAATTTCAGGGTCAAATGAAAACGTCTTGGTTTTTCCTTCAATAGAAAATGCTTTGCAAGAACTATCTAAAATTACAGATCATGTATATATTTCGGGTGGGGGGCAAATCTATGAAAGCCTTATTGAAAAAGCAGATATAATTCATCTATCTACTATTCATGTTGAGGTTGAAGGTGATATTAAATTCCCTATATTACCTGAAGGTTTCAACTTGGTTTTTGAACAGTTTTTTGTGTCTAATATAAATTATACATATCAAATTTGGAAAAAAGGCTAA", "fmax": "1008", "accession": "GU067642.1", "fmin": "534", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Salmonella enterica", "NCBI_taxonomy_id": "28901", "NCBI_taxonomy_cvterm_id": "35672"}, "protein_sequence": {"accession": "ACZ52983.1", "sequence": "MKISLISAVSENGVIGSGPDIPWSAKGEQLIFKALTYNQWLLVGRKTFDSMGVLPNRKYAVVSKNGISGSNENVLVFPSIENALQELSKITDHVYISGGGQIYESLIEKADIIHLSTIHVEVEGDIKFPILPEGFNLVFEQFFVSNINYTYQIWKKG"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA32", "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": "42460", "model_name": "dfrA32", "model_type_id": "40292"}, "3262": {"model_id": "3262", "ARO_accession": "3004554", "model_param": {"blastp_bit_score": {"param_value": "300", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene isolated from canine Escherichia coli infection", "model_sequences": {"sequence": {"5118": {"dna_sequence": {"partial": "0", "sequence": "ATGGCTGCAAGAGCGAAAAATGGCGTAATCGGTTGCGGTCCTAACATTCCTTGGTCTGCCAAAGGGGAACAGCTTCTTTTCAAAGCACTGACCTATAACCAATGGCTTTTGGTAGGGCGCAAAACATTTGAGTCTATGGGGCCGCTGCCCAATAGGAAATACGCGGTTGTTACCCGCTCAAACTGGACAGCGGCTAATGAAAACGTAGTGGTTTTCCCGTCGATTGACGAAGCGATGGGTAGATTAGGCGAGATCACTGACCATGTCATCGTCGCCGGTGGTGGAGAAATCTACCATGAAACGATACCCATGGCCTCTACTCTGCATGTGTCGACAATCGACGTTGAGCCAGAGGGAGACGTTTTCTTTCCGAACATTCCTGGGAAGTTTGATGTCGTTTTTGAGCAACAATTTACATCAAACATTAACTATTGCTATCAAATCTGGCAAAAGGGTTAA", "fmax": "590", "accession": "KX118301.1", "fmin": "131", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "ANN23980.1", "sequence": "MAARAKNGVIGCGPNIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGPLPNRKYAVVTRSNWTAANENVVVFPSIDEAMGRLGEITDHVIVAGGGEIYHETIPMASTLHVSTIDVEPEGDVFFPNIPGKFDVVFEQQFTSNINYCYQIWQKG"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrA29", "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": "42459", "model_name": "dfrA29", "model_type_id": "40292"}, "3272": {"model_id": "3272", "ARO_accession": "3004571", "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": "PNGM-1 is a subclass B3 metallo-beta-lactamase first identified from a deep-sea sediment meta-genome. PNGM-1 is shown to reduce susceptibility to extended- and broad-spectrum cephalosporins, carbapenems, and penicillins. PNGM-1 is a novel metallo-beta-lactamase which predates the current antibiotic era.", "model_sequences": {"sequence": {"5133": {"dna_sequence": {"partial": "0", "sequence": "ATGGCAGGTGGAAAAGTAACCTCATCAACAGGTATCGCACCCAAACGGTACGTCTATTATCCAGGCAGTGAAGAATTGGGGCCCGATGAGATTCGGGTTATTGCTTGTGGCACAGGCATGCCTACGGCGCGTCGTGCTCAAGCAGCGGCCGCCTGGGTGGTAGAGCTAGGCAACGGTGACAAATTCATCGTCGACATTGGCAGCGGCTCAATGGCCAACATCCAATCGTTGATGATCCCGGCTAATTATTTGACCAAGATTTTTCTGACGCATTTGCACACCGACCACTGGGGCGACCTGGTGTCTATGTGGGCAGGCGGTTGGACAGCCGGGCGCACGGATCCGTTAGAGGTATGGGGACCAAGCGGTTCACGCGAAGATATGGGCACAAAGTACGCCGTCGAGCACATGCTCAAGGCGTACAATTGGGACTATATGACACGAGCCGTGACGATTAATCCCCGCCCCGGAGATATCAATGTTCACGAGTTCGACTATCGTGCCCTCAACGAGGTTGTCTATCAAGAGAACGGCGTCACTTTCCGCTCCTGGCCCTGTATTCACGCGGGAGACGGACCGGTCAGCTTTGCCCTAGAGTGGAATGGCTACAAGGTGGTTTTTGGCGGAGACACCGCCCCCAATATTTGGTACCCAGAATACGCCAAGGGTGCTGACCTGGCGATCCATGAGTGCTGGATGACCTCCGATCAAATGATGACAAAATATAACCAGCCGGCACAGCTTGCACTGCGCATCAATCTGGACTTTCACACCTCAGCGCAATCCTTTGGCCAGATTATGAATATGGTGCAGCCACGCCATGCCGTAGCCTATCACTTTTTCAACGATGATGACACGCGGTACGATATCTATACTGGCGTAAGAGAGAACTATGCCGGTCCCCTTTCAATGGCTACCGACATGATGGTGTGGAATATCACTCGAGACGCAGTCACCGAGCGTATGGCTGTCTCGCCGGATCATGCGTGGGATGTGGCAGGTCCTTCCGAAGATCTGGCGCCAGATCGGAATAGAGCCTCGGAGTACACGCAGTATATCCTCGACGGCCGTCTCAATGTCGACGAGGCCAATGCCCATTGGAAGCAGGAGTTCATGGGTCGTACTGGATTAACGACCGAGGATTTGGGAGTGGGAAGCTAA", "fmax": "1161", "accession": "MF445022.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "uncultured bacterium", "NCBI_taxonomy_id": "77133", "NCBI_taxonomy_cvterm_id": "36791"}, "protein_sequence": {"accession": "AWN09461.1", "sequence": "MAGGKVTSSTGIAPKRYVYYPGSEELGPDEIRVIACGTGMPTARRAQAAAAWVVELGNGDKFIVDIGSGSMANIQSLMIPANYLTKIFLTHLHTDHWGDLVSMWAGGWTAGRTDPLEVWGPSGSREDMGTKYAVEHMLKAYNWDYMTRAVTINPRPGDINVHEFDYRALNEVVYQENGVTFRSWPCIHAGDGPVSFALEWNGYKVVFGGDTAPNIWYPEYAKGADLAIHECWMTSDQMMTKYNQPAQLALRINLDFHTSAQSFGQIMNMVQPRHAVAYHFFNDDDTRYDIYTGVRENYAGPLSMATDMMVWNITRDAVTERMAVSPDHAWDVAGPSEDLAPDRNRASEYTQYILDGRLNVDEANAHWKQEFMGRTGLTTEDLGVGS"}}}}, "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."}, "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."}, "42479": {"category_aro_name": "PNGM beta-lactamase", "category_aro_cvterm_id": "42479", "category_aro_accession": "3004570", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "PNGM is a family of metallo-beta-lactamases first identified from a deep-sea sediment metagenome and shown to reduce antibiotic susceptibility by hydrolysis of penicillins, carbapenems and extended- and broad-spectrum cephalosporins."}, "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": "PNGM-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": "42480", "model_name": "PNGM-1", "model_type_id": "40292"}, "3264": {"model_id": "3264", "ARO_accession": "3004556", "model_param": {"blastp_bit_score": {"param_value": "200", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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 dihydrofolate reductase and trimethoprim resistance gene identified on an integron in multidrug-resistant gram-negative bacteria", "model_sequences": {"sequence": {"5120": {"dna_sequence": {"partial": "1", "sequence": "ATGGACCAAGGTAGCAATGAAGTCGGTAATCCAGTTGCGGGCCAGTTTTCGTTCCCATCGAACGCCGCGTTTAGTATGGGAGATCGCGTGCGCAAGAAATCGGGCGCCGCTTGGCAAGGTCAGATTGTCGGGTGGTACTGCACAAAGTTGACCCCTGAAGGCTACGCTGTCGAGTCTGAGGCTCACCCTGGCTCGGTACAGATTTATCCTGTTGCGGCGCTTGAACGCATCAACGGAGTTCAAGGTTGA", "fmax": "1296", "accession": "GU295656.1", "fmin": "1047", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Aeromonas hydrophila", "NCBI_taxonomy_id": "644", "NCBI_taxonomy_cvterm_id": "36810"}, "protein_sequence": {"accession": "ADB54781.1", "sequence": "MDQGSNEVGNPVAGQFSFPSNAAFSMGDRVRKKSGAAWQGQIVGWYCTKLTPEGYAVESEAHPGSVQIYPVAALERINGVQG"}}}}, "ARO_category": {"36476": {"category_aro_name": "iclaprim", "category_aro_cvterm_id": "36476", "category_aro_accession": "3000337", "category_aro_class_name": "Antibiotic", "category_aro_description": "Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus."}, "36327": {"category_aro_name": "trimethoprim", "category_aro_cvterm_id": "36327", "category_aro_accession": "3000188", "category_aro_class_name": "Antibiotic", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic."}, "36408": {"category_aro_name": "brodimoprim", "category_aro_cvterm_id": "36408", "category_aro_accession": "3000269", "category_aro_class_name": "Antibiotic", "category_aro_description": "Brodimoprim is a structural derivative of trimethoprim and an inhibitor of bacterial dihydrofolate reductase. The 4-methoxy group of trimethoprim is replaced with a bromine atom."}, "37617": {"category_aro_name": "trimethoprim resistant dihydrofolate reductase dfr", "category_aro_cvterm_id": "37617", "category_aro_accession": "3001218", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance."}, "36310": {"category_aro_name": "diaminopyrimidine antibiotic", "category_aro_cvterm_id": "36310", "category_aro_accession": "3000171", "category_aro_class_name": "Drug Class", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "36423": {"category_aro_name": "tetroxoprim", "category_aro_cvterm_id": "36423", "category_aro_accession": "3000284", "category_aro_class_name": "Antibiotic", "category_aro_description": "Tetroxoprim is a trimethoprim derivative that inhibits bacterial dihydrofolate reductase."}}, "ARO_name": "dfrB7", "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": "42461", "model_name": "dfrB7", "model_type_id": "40292"}, "3267": {"model_id": "3267", "ARO_accession": "3004561", "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."}, "snp": {"param_type": "single resistance variant", "param_value": {"8659": "P108L"}, "clinical": {"8659": "P108L"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Mutations in murG which confer resistance to vancomycin in Clostridium difficile", "model_sequences": {"sequence": {"5124": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAACTGAAAATAGTAATGACGGGTGGAGGTTCTGCTGGACATGTTACCCCTAATTTAGCACTTGTGCCAAAACTAAAGGAGCTAGGATACGAAATAGAGTATATAGGAACAAAGGATGGGATAGAAAGAAGTATAATTGAAAAAGAAAATATAAAGTATAATTGTATATCCAGTGGAAAATTAAGAAGATATATTGATATTAAAAATTTTTCAGATCCTTTTAAGGTTATTTTAGGGATATTTCAATCTGTTAGTATATTAAGGAAGAAAAAGCCTAACATAGTCTTTTCTAAAGGAGGTTTTGTGTCAGTTCCTGTGGTTATAGCAGCACATTTTTGCAGAATACCGGTAATAGCTCATGAATCAGATATAACACCTGGACTTGCAAATAGGATAGCAGTTCCTTACTGCACAAAAGTTTGTGCTACATTTCCAGAATCTCTTAACAATATAAAAGGGAATAAGGGAATATTAACAGGTACTCCTATACGAGATGAGTTATTTAAGGGAAGTAAAATTAAGGGACTTGAAATATGTGGATTTACAGGTGAGAAGCCAGTACTTATGATTATAGGTGGAAGTTTAGGATCAAAGATTATAAATGATACAGTTCGTGAAGCTTTAAATAAGCTTATAAAAAAATATGATATAGTTCATATTTGTGGAAAGGGAAATATAGATGAAGCTTTAAGTAAACTTAAGGGGTATAAGCAATTTGACTATATATCAACTGAACTTCCTCATGTAATGAATGCTGCAGATTTAGTTATTTCAAGAGCAGGGGCTAATGCTATTTTTGAGCTTTTAGCATTAAAAAAGCCTAATTTATTGATCCCATTATCTAAAAAATCAAGCAGGGGAGATCAGATTTTAAATGCTATGTCATTTGAAAAAAATGGTTACAGTATGGTGGTTCAGGAAGATGACTTAACACCAACGTTGCTTGTAGAGAAGGTCATTAAACTTGAAAGCGATAAGGAAAAATACAAGAAAGCTATGAATTCAAGTCCTGTAAAAAATGGTGTGGAAAATATAATTAAAGTTATTGATAAATATAAAAAATGTAAAATATAG", "fmax": "2324860", "accession": "NC_003030.1", "fmin": "2323780", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridium acetobutylicum ATCC 824", "NCBI_taxonomy_id": "272562", "NCBI_taxonomy_cvterm_id": "42468"}, "protein_sequence": {"accession": "NP_348848.1", "sequence": "MKKLKIVMTGGGSAGHVTPNLALVPKLKELGYEIEYIGTKDGIERSIIEKENIKYNCISSGKLRRYIDIKNFSDPFKVILGIFQSVSILRKKKPNIVFSKGGFVSVPVVIAAHFCRIPVIAHESDITPGLANRIAVPYCTKVCATFPESLNNIKGNKGILTGTPIRDELFKGSKIKGLEICGFTGEKPVLMIIGGSLGSKIINDTVREALNKLIKKYDIVHICGKGNIDEALSKLKGYKQFDYISTELPHVMNAADLVISRAGANAIFELLALKKPNLLIPLSKKSSRGDQILNAMSFEKNGYSMVVQEDDLTPTLLVEKVIKLESDKEKYKKAMNSSPVKNGVENIIKVIDKYKKCKI"}}}}, "ARO_category": {"36220": {"category_aro_name": "glycopeptide antibiotic", "category_aro_cvterm_id": "36220", "category_aro_accession": "3000081", "category_aro_class_name": "Drug Class", "category_aro_description": "Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "35947": {"category_aro_name": "vancomycin", "category_aro_cvterm_id": "35947", "category_aro_accession": "0000028", "category_aro_class_name": "Antibiotic", "category_aro_description": "Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme."}, "42466": {"category_aro_name": "murG transferase", "category_aro_cvterm_id": "42466", "category_aro_accession": "3004560", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "murG acetylglucosaminyltransferase enzymes inhibited by vancomycin. Mutations in murG confer resistance to vancomycin through antibiotic target alteration."}}, "ARO_name": "Clostridium difficile murG with mutation conferring resistance to vancomycin", "model_type": "protein variant model", "model_description": "The protein variant model is an AMR detection model. 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.", "ARO_id": "42467", "model_name": "Clostridium difficile murG with mutation conferring resistance to vancomycin", "model_type_id": "40293"}, "3266": {"model_id": "3266", "ARO_accession": "3004559", "model_param": {"blastp_bit_score": {"param_value": "400", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment 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": "CAM-1 is a CAM (Central Alberta Metallo) beta-lactamase and carbapenemase identified from 4 clinical isolates of Pseudomonas aeruginosa from a Canadian hospital", "model_sequences": {"sequence": {"5123": {"dna_sequence": {"partial": "0", "sequence": "ATGAAATCAACTGCAATTATTTTATTTTTACTCGTTTTTTCGCTCGGCGTTTTCGGGCAAACGGGCGATGCGCTGAAAATCTCTCAACTGTCGGGCGATTTTTATATTTTTACGACTTATCAAACCTATAAAGACGCAAAAGTTTCCGCCAACGGAATGTATGTCGTGACCGACGAAGGCGTTGTTTTGATCGACACGCCGTGGGATGAAACTCAGCTTCAGCCGCTTCTCAATTACATCAAGGAAAAGCACAACAAGGATGTCGTGATGAGCGTTTCGACGCATTTTCACGAAGACCGCACGAACGGCATCGAATTTTTGAGGACAAAAGGCGTGAAAACCTACACGACCAAGAAAACCGACGAGCTTTCGCAGAAAAAAGGTTACGAACGCGCCGAATTTTTGCTCGAAAAAGACACGGAATTCAAGATCGGGCAATACAAATTTCAAACCTACTATCCCGGCGAAGGTCACGCGCCCGACAATATCGTGGTCTGGTTTCCGAACGAAAGAATTCTTTACGGCGGTTGTTTCATAAAAAGCACCGAAGCCGAAGACATCGGGAATTTGTCCGATGCAAATATCGATGAATGGTCAAACTCGATCAAAAACGTGCAGAAAAAATTCAAGAACCCGAAATTCGTAATTCCCGGTCACGACGGATGGGCAAGCACGAAATCACTCAAACACACATTAAAACTTATCAAGAAAACCCGTAAAAAATAA", "fmax": "67829", "accession": "MG430339.1", "fmin": "67103", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AVX51087.1", "sequence": "MKSTAIILFLLVFSLGVFGQTGDALKISQLSGDFYIFTTYQTYKDAKVSANGMYVVTDEGVVLIDTPWDETQLQPLLNYIKEKHNKDVVMSVSTHFHEDRTNGIEFLRTKGVKTYTTKKTDELSQKKGYERAEFLLEKDTEFKIGQYKFQTYYPGEGHAPDNIVVWFPNERILYGGCFIKSTEAEDIGNLSDANIDEWSNSIKNVQKKFKNPKFVIPGHDGWASTKSLKHTLKLIKKTRKK"}}}}, "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."}, "36989": {"category_aro_name": "cefotaxime", "category_aro_cvterm_id": "36989", "category_aro_accession": "3000645", "category_aro_class_name": "Antibiotic", "category_aro_description": "Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups."}, "36309": {"category_aro_name": "imipenem", "category_aro_cvterm_id": "36309", "category_aro_accession": "3000170", "category_aro_class_name": "Antibiotic", "category_aro_description": "Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes."}, "35977": {"category_aro_name": "ceftazidime", "category_aro_cvterm_id": "35977", "category_aro_accession": "0000060", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections."}, "35927": {"category_aro_name": "cefoxitin", "category_aro_cvterm_id": "35927", "category_aro_accession": "0000008", "category_aro_class_name": "Antibiotic", "category_aro_description": "Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases."}, "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."}, "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."}, "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."}, "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."}, "42464": {"category_aro_name": "CAM beta-lactamase", "category_aro_cvterm_id": "42464", "category_aro_accession": "3004558", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "CAM (Central Alberta Metallo) beta-lactamases are class B metallo-beta-lactamases and carbapenemases found to confer resistance to broad spectrum antibiotics in Pseudomonas aeruginosa."}, "35995": {"category_aro_name": "piperacillin", "category_aro_cvterm_id": "35995", "category_aro_accession": "0000078", "category_aro_class_name": "Antibiotic", "category_aro_description": "Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria."}, "35994": {"category_aro_name": "tazobactam", "category_aro_cvterm_id": "35994", "category_aro_accession": "0000077", "category_aro_class_name": "Adjuvant", "category_aro_description": "Tazobactam is a compound which inhibits the action of bacterial beta-lactamases."}, "40636": {"category_aro_name": "ceftolozane", "category_aro_cvterm_id": "40636", "category_aro_accession": "3003927", "category_aro_class_name": "Antibiotic", "category_aro_description": "a 5th generation cephalosporin antibiotic"}, "36984": {"category_aro_name": "doripenem", "category_aro_cvterm_id": "36984", "category_aro_accession": "3000640", "category_aro_class_name": "Antibiotic", "category_aro_description": "Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis."}, "35990": {"category_aro_name": "meropenem", "category_aro_cvterm_id": "35990", "category_aro_accession": "0000073", "category_aro_class_name": "Antibiotic", "category_aro_description": "Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem."}}, "ARO_name": "CAM-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": "42465", "model_name": "CAM-1", "model_type_id": "40292"}, "3269": {"model_id": "3269", "ARO_accession": "3004563", "model_param": {"blastp_bit_score": {"param_value": "2500", "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."}, "snp": {"param_type": "single resistance variant", "param_value": {"8679": "S488P", "8678": "H502N", "8677": "R505K", "8680": "S498T"}, "clinical": {"8679": "S488P", "8678": "H502N", "8677": "R505K", "8680": "S498T"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Point mutations in the rpoB region of Clostridium (Clostridioides) difficile which confer resistance to rifampin and rifampicin antibiotics", "model_sequences": {"sequence": {"5126": {"dna_sequence": {"partial": "0", "sequence": "ATGGTACATCCTGTCCAGGTTGGTAAAAGAACAAGAATGAGCTTTTCCAGACTTAAAGAAATAGGCCACATGCCTAATTTAATTGAGGTTCAGCTAGATTCCTACAATTGGTTTTTGAAAGAAGGATTACAAGAGGTATTTGATGATATTAATCCTATTCAAGATTATACTGCTAACCTTAATTTGGAATTTGTAGGATATAAGTTAGATATGGATAATATCAAATATTCTGTAGAGGAATGTAAAGAAAGAGATGCAACTTACGCAGCACCTTTAAAAGTAAAAGTAAGGCTAATTAACAAAGAAACTGGTGAAGTTAAAGAGCAAGAAGTTTTTATGGGAGATTTCCCTCTTATGACGGAGCAAGGAACCTTTATAATTAATGGTGCAGAGAGAGTTATAGTTAGCCAACTTGTAAGATCACCAGGTGTATATTATGATCTTTCAGTTGATAAAACAGGAAAAAATCTTTTTTCTTCAACTGTAATACCTAATAGAGGAGCTTGGCTAGAATATGAAACTGACTCTAACAATGTAATATACGTTAGAATAGATAAAACTAGAAAGTTACCCATAACTATTCTTATTAGAGCCATGGGTTATGGTACAGACGCAGAAATTACTAATTTCTTTGGAGAGGATGAAAGGCTAAAAGCCACAATTGAAAAAGATAATACAAAGACTCATGAAGAGGCTTTGCTTGAAATATATAAAAGGTTACGACCGGGAGAACCTCCTACAGTGGATAGTGCCCAATCACTAATTGAATCTTTATTTTTTGATGCGAAAAGATATGATCTTTCAAGAGTTGGAAGATACAAATTCAATAAGAAGTTATCATTACACCTAAGAATTGCTAATCAGATAGCAGCACAGGATGTAGTTAATCCAGATACAGGAGAAATTCTTATCCAAAAAGGTGAAAAGATAAATAGAGAAAAGGCAGTAGAAATCCAACAGTGTGGAATAAATGTAGTAGATATCCAAATTGAAGATATAGTTTTAAGAGTTATAGGTAATAACTTTGTAGACATACGTAGTTTTATTGACTTTGATATAGATGATTTAAATATAAAAGAAAGTGTTCATTATCCCACTTTAAAGAAAATTTTAGATAATTATAGTGATGAGGAAAGTATTAAGGAACAAATAAGAAAGAACATCCATGAATTAATTCCAAAACATATAGTTAGAGATGATATGTATGCTACCATTAGCTATGAGTTGGGATTAGCATATGGAGTAGGTCATACTGATGACATAGACCATCTTGGAAATAGAAGACTTAGATCTGTTGGTGAATTACTTCAAAATCAATTTAGAATAGGTCTCTCAAGAATGGAGAGAGTGGTTAAGGAAAGAATGACCATACAGGATCAGGAAGTTATAACACCTCAAGCTCTTATAAATATAAGACCAGTAGCTGCGTCTATAAAAGAGTTTTTTGGAAGTTCTCAACTTTCTCAATTCATGGATCAAACTAATCCATTGTCAGAGCTTACCCATAAGAGGAGACTATCTGCTTTAGGACCAGGCGGACTTTCAAGAGAAAGAGCTGGATTTGAAGTCAGGGATGTTCATCACTCACATTATGGAAGAATGTGTCCAATAGAGACGCCAGAAGGACCTAACATAGGACTTATTAACTCTCTAGCTACATATGCAAGAGTTAATCAATATGGCTTTATAGAAACGCCTTATAGAAAAGTAGATAAAGAAAATAAGAGAGTTACAAATGAAATTGTATATATGACAGCAGACGAGGAAGATGAATATTTAATAGGTAGGGCAAACGAGCCTATTGATGAAAATGGTAATTTTATAGATAATAAAATTACAGTTAGAGATAAAGAAGATGTTATTGTAGTACCTGGTCAAGACGTTGATTATATGGATGTGTCTTCAAGGCAATTAGTTTCTGTAGCTACAGCTATGATACCATTCCTTGAAAATGATGATGCCAGCCGTGCACTTATGGGATCAAATATGCAAAGGCAGGCAGTTCCACTTTTGAAACCACAAGCACCTATTGTAGGAACAGGTATTGAATACAAGGCTGCAGTAGATTCAGGAGTACTTCCTAAAGCTAGAAATGCAGGCGTTGTCTCTTATGTATGTGCTAACGAAGTAAGGGTTAAGAGAGACTCAGATGGAGGAACAGATATTTATAGACTTCTTAAGTTCCAGAGATCTAACCAATGCACATGCATCAATCAAAGACCTATAGTTGAAAAAGGGGAAGTAGTTAAAAAGGGAACAGTTTTAGCAGATGGACCTTCTACAGATCTTGGAGAAATAGCACTTGGAAAAAATATTAGAATGGGATTTACAACTTGGGAAGGATATAATTATGAAGACGCAATGCTTATATCTGAAGAGTTAGTAAAAAAAGATGTATTTACATCAATACATCTAGAGGAATACGAATCTGAGGCTAGAGATACAAAATTAGGACCAGAGGAAATTACAAGAGATATACCAAATGTAGGAGAAGATGCATTAAAGGATATAGATGAAAGAGGAATTATAAGAATAGGTGCAGAAGTTAGAGCAGGAGATATATTAGTAGGTAAAGTAACACCTAAGGGGGAAACTGAACTTACAGCAGAAGAAAGGCTTTTAAGAGCAATATTTGGCGAAAAGGCCAGAGAAGTTAGAGATACGTCCCTTAGAGTACCACATGGTGAAGCGGGCATAATTGTAGATGTAAAAGTATTTACAAGAGAAAATGGAGATGAGCTTTCACCAGGAGTTAACAAATTAGTTAGATGTTATATAGCTCAGAAGAGAAAGATATCTGTAGGAGATAAAATGGCAGGAAGACACGGAAATAAAGGTGTTATTTCTAGAGTACTACCAGAGGAAGATATGCCTTTCCTACCAGATGGAAGACCTCTTCAGATATGCTTAAATCCACTTGGTGTACCTTCACGTATGAATATAGGTCAGGTATTAGAAGTTCATTTAGGATGGGCTGCCAGTAAATTAGGATGGCATGTAGCGACTCCAGTATTTGATGGAGCCACAGAAGAAGATATATTGGAATGCTTGAAAAAAGCAGGGTATAGAGAAGACGGAAAAACAATACTATATGATGGTAGAACAGGAGAAGAATTTAATAGGCCTGTAACTGTAGGATATATGTATATCTTAAAATTAGCACATTTGGTTGACGATAAGATCCATGCAAGATCTACAGGACCATATTCGTTAGTAACTCAACAGCCATTGGGTGGTAAAGCTCAATTTGGTGGCCAAAGATTTGGTGAAATGGAAGTTTGGGCATTAGAGGCATATGGAGCAGCTCATACACTTCAGGAAATATTGACAGTTAAGTCAGACGATGTAGTTGGAAGAGTTAAAACTTATGAAGCTATTGTAAAAGGTGAAAATATACCAGAACCGGGAATTCCAGAATCATTTAAGGTTCTGATAAAGGAACTTCAAGCTTTATGCTTGGATGTAAAAGTATTAAATGATAATAAAGAGGAAATCAAACTTAAAGAGTCTGTGGACGAAGAGATGGAAAAACTAGATGTAAATATTGAAGGAAAAGAAGATTCTACTGATTTACCTCAAGAACAAAATGATGACTATAATACTGAGCAAGAAGAAAACAATGATAGTGAAAATGACAGCGATGAAGATCTTGATTTAGATTATGAAGATCTTACTTTAGATGATTTGCAGAGTGATTTAGAAATAGATGATTTTAATGATGAACATTAG", "fmax": "4458527", "accession": "NC_014328.1", "fmin": "4454798", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridium", "NCBI_taxonomy_id": "1485", "NCBI_taxonomy_cvterm_id": "37054"}, "protein_sequence": {"accession": "WP_013240699.1", "sequence": "MVHPVQVGKRTRMSFSRLKEIGHMPNLIEVQLDSYNWFLKEGLQEVFDDINPIQDYTANLNLEFVGYKLDMDNIKYSVEECKERDATYAAPLKVKVRLINKETGEVKEQEVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDLSVDKTGKNLFSSTVIPNRGAWLEYETDSNNVIYVRIDKTRKLPITILIRAMGYGTDAEITNFFGEDERLKATIEKDNTKTHEEALLEIYKRLRPGEPPTVDSAQSLIESLFFDAKRYDLSRVGRYKFNKKLSLHLRIANQIAAQDVVNPDTGEILIQKGEKINREKAVEIQQCGINVVDIQIEDIVLRVIGNNFVDIRSFIDFDIDDLNIKESVHYPTLKKILDNYSDEESIKEQIRKNIHELIPKHIVRDDMYATISYELGLAYGVGHTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYARVNQYGFIETPYRKVDKENKRVTNEIVYMTADEEDEYLIGRANEPIDENGNFIDNKITVRDKEDVIVVPGQDVDYMDVSSRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAAVDSGVLPKARNAGVVSYVCANEVRVKRDSDGGTDIYRLLKFQRSNQCTCINQRPIVEKGEVVKKGTVLADGPSTDLGEIALGKNIRMGFTTWEGYNYEDAMLISEELVKKDVFTSIHLEEYESEARDTKLGPEEITRDIPNVGEDALKDIDERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGDELSPGVNKLVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAASKLGWHVATPVFDGATEEDILECLKKAGYREDGKTILYDGRTGEEFNRPVTVGYMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGIPESFKVLIKELQALCLDVKVLNDNKEEIKLKESVDEEMEKLDVNIEGKEDSTDLPQEQNDDYNTEQEENNDSENDSDEDLDLDYEDLTLDDLQSDLEIDDFNDEH"}}}}, "ARO_category": {"36308": {"category_aro_name": "rifampin", "category_aro_cvterm_id": "36308", "category_aro_accession": "3000169", "category_aro_class_name": "Antibiotic", "category_aro_description": "Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections."}, "36673": {"category_aro_name": "rifapentine", "category_aro_cvterm_id": "36673", "category_aro_accession": "3000534", "category_aro_class_name": "Antibiotic", "category_aro_description": "Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy."}, "36669": {"category_aro_name": "rifabutin", "category_aro_cvterm_id": "36669", "category_aro_accession": "3000530", "category_aro_class_name": "Antibiotic", "category_aro_description": "Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis."}, "36192": {"category_aro_name": "peptide antibiotic", "category_aro_cvterm_id": "36192", "category_aro_accession": "3000053", "category_aro_class_name": "Drug Class", "category_aro_description": "Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics."}, "36349": {"category_aro_name": "rifamycin-resistant beta-subunit of RNA polymerase (rpoB)", "category_aro_cvterm_id": "36349", "category_aro_accession": "3000210", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin."}, "35998": {"category_aro_name": "antibiotic target replacement", "category_aro_cvterm_id": "35998", "category_aro_accession": "0001002", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "36656": {"category_aro_name": "rifaximin", "category_aro_cvterm_id": "36656", "category_aro_accession": "3000517", "category_aro_class_name": "Antibiotic", "category_aro_description": "Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase."}, "36296": {"category_aro_name": "rifamycin antibiotic", "category_aro_cvterm_id": "36296", "category_aro_accession": "3000157", "category_aro_class_name": "Drug Class", "category_aro_description": "Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs."}}, "ARO_name": "Clostridium difficile rpoB with mutation conferring resistance to rifampicin", "model_type": "protein variant model", "model_description": "The protein variant model is an AMR detection model. 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.", "ARO_id": "42470", "model_name": "Clostridium difficile rpoB with mutation conferring resistance to rifampicin", "model_type_id": "40293"}, "3268": {"model_id": "3268", "ARO_accession": "3004562", "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."}, "snp": {"param_type": "single resistance variant", "param_value": {"8673": "D426V", "8672": "S416A", "8671": "E466V", "8670": "R447L", "8675": "E466K", "8674": "R447K", "8669": "D426N"}, "clinical": {"8673": "D426V", "8672": "S416A", "8671": "E466V", "8670": "R447L", "8675": "E466K", "8674": "R447K", "8669": "D426N"}, "param_type_id": "36301", "param_description": "A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type. The most common type encoded in the CARD is an amino acid substitution gleaned from the literature with format [wild-type][position][mutation], e.g. R184Q. When present in the associated gene or protein, a single resistance variant confers resistance to an antibiotic drug or drug class. Single resistance variants are used by the protein variant and rRNA mutation models to detect antibiotic resistance from submitted sequences."}}, "ARO_description": "Point mutations in gyrB of Clostridium (Clostridioides) difficile conferring resistance to fluoroquinolone antibiotics", "model_sequences": {"sequence": {"5125": {"dna_sequence": {"partial": "0", "sequence": "ATGATGCAAGAAAAAAAGCAAACTTATGATGAAAATCAAATACAAGTATTAGAAGGTCTTGAAGCTGTTAGAAAAAGACCTGGAATGTATATTGGAAGTACTAGTTCTAGGGGGCTTCATCATTTAGTGTATGAGATAGTTGATAATAGCATAGATGAGGCATTGGCAGGATATTGCGATAAAATAAATGTAATTATACATAAAGATAATTCTATAACAGTTACGGATAATGGTAGAGGAATGCCTGTTGGAATGCACCATAAAATGAAGAAACCAACTGTAGAAGTTATAATGACTATACTACATGCAGGAGGGAAATTTGGTGGTGGAGGATACAAAGTTTCCGGCGGACTTCATGGAGTTGGAGCATCAGTTGTAAATGCTTTATCTGAAATCTGTGAAGTTGAAGTAAAAAGAGAAAGCCATATATGGAGACAGGTATTTAAAAGAGGAAAAGTAGCAAGCGGACTTGACATAATAGGTGATAGTGAGGAGCACGGAACAAAAATTCACTTTAAACCAGATGCAGAAATATTTGATGAAATAGAATATGATTATGATACATTGGCTCAAAGGCTTAGAGAATTGGCATTTTTAAACAAGGGTATAAAAATAAGGTTAGAAGATGAGAGAGATGATAAAGAAGAAATATTTCACTATGAAGGTGGAATAAAGTCCTTTGTAACTTATCTTAATAGAAATAAACAACCAATTCATAAAGAGCCTATATACGTAGAAGGCAAAAAAGATGACTACTCTGTAGAAATTGCTATTCAATACAATGATGGGTATACTGAAAATATTTTTGCTTTTGCTAATAACATAGATACAGTAGAAGGTGGAACTCATTTAGCTGGATTTAAGTCAGCACTTACTAGAGTATTTAATGATTATGCAAAAAAATTTGGTATATTAAAAGAAAATGATAAGAACCTATCAGGAGAAGATATAAGGGAAGGCCTTACTGCAGTTATATCTGTAAAACTTGTAGACCCTCAATTTGAAGGCCAGACGAAAACAAAACTAGGAAATAGTGAAGTGCGTGGTATAGTTGACAGCATAATGGGAGAGTCCTTAAATAATTTTTTACAGGAAAATCCTCAAGTAGCAAAGATGATACTTGATAAATCACTTATGGCATCACGTGCTAGAGAAGCGGCAAGAAAAGCAAGAGAGCTTACAAGACGTAAATCTATACTTGAAAATACTTCTCTTCCAGGAAAATTAGCAGATTGTTCATCTAAAGATCCTTCTGAATGTGAAATATATTTAGTCGAGGGTGATTCTGCAGGTGGATCTGCAAAACAAGGTAGAAATAGAAAATTTCAAGCTATACTTCCGCTACGTGGTAAAATAATGAATGTTGAGAAACAAAGGCTTGACAAAATACTTGGCTATGAAGAAATAAGAGCTATGATAACGGCATTTGGAGCAGGTATAGGAAAAGACTTTGATGTAAATAAAATAAGATACAATAAAATAATAATAATGACAGATGCAGATGTAGATGGTGCGCACATAAGAACATTATTACTTACTTTTTTCTTCAGATATATGAAGGAACTTGTTGAAAAATGTCACGTTTATATAGCTCAACCACCTTTATATAGAGTAGCTAAAGGGAAGAAGGAATACTACGCATATTCAGATGATGAATTAGATGTATTGCTTACTGAAATAGGTGGGAAAGACAGTAATGTAGATATACAAAGATATAAAGGACTTGGAGAAATGGATTCAGAGCAACTTTGGGATACTACAATGAATCCTGAAACAAGGACTCTTATTCAAGTAAATGTAGAGGACACTATGGCTGCTGATGAAATCTTTACTATACTTATGGGTGACAAGGTAGAACCTCGTAGAAATTTTATACAAGAAAATGCTAAAAAAGTTGTAAACTTAGATATATAA", "fmax": "6430", "accession": "NC_014328.1", "fmin": "4516", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Clostridium", "NCBI_taxonomy_id": "1485", "NCBI_taxonomy_cvterm_id": "37054"}, "protein_sequence": {"accession": "WP_013236720.1", "sequence": "MMQEKKQTYDENQIQVLEGLEAVRKRPGMYIGSTSSRGLHHLVYEIVDNSIDEALAGYCDKINVIIHKDNSITVTDNGRGMPVGMHHKMKKPTVEVIMTILHAGGKFGGGGYKVSGGLHGVGASVVNALSEICEVEVKRESHIWRQVFKRGKVASGLDIIGDSEEHGTKIHFKPDAEIFDEIEYDYDTLAQRLRELAFLNKGIKIRLEDERDDKEEIFHYEGGIKSFVTYLNRNKQPIHKEPIYVEGKKDDYSVEIAIQYNDGYTENIFAFANNIDTVEGGTHLAGFKSALTRVFNDYAKKFGILKENDKNLSGEDIREGLTAVISVKLVDPQFEGQTKTKLGNSEVRGIVDSIMGESLNNFLQENPQVAKMILDKSLMASRAREAARKARELTRRKSILENTSLPGKLADCSSKDPSECEIYLVEGDSAGGSAKQGRNRKFQAILPLRGKIMNVEKQRLDKILGYEEIRAMITAFGAGIGKDFDVNKIRYNKIIIMTDADVDGAHIRTLLLTFFFRYMKELVEKCHVYIAQPPLYRVAKGKKEYYAYSDDELDVLLTEIGGKDSNVDIQRYKGLGEMDSEQLWDTTMNPETRTLIQVNVEDTMAADEIFTILMGDKVEPRRNFIQENAKKVVNLDI"}}}}, "ARO_category": {"37244": {"category_aro_name": "fluoroquinolone resistant gyrB", "category_aro_cvterm_id": "37244", "category_aro_accession": "3000864", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones."}, "36271": {"category_aro_name": "clorobiocin", "category_aro_cvterm_id": "36271", "category_aro_accession": "3000132", "category_aro_class_name": "Antibiotic", "category_aro_description": "Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling."}, "36242": {"category_aro_name": "aminocoumarin antibiotic", "category_aro_cvterm_id": "36242", "category_aro_accession": "3000103", "category_aro_class_name": "Drug Class", "category_aro_description": "Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling."}, "36250": {"category_aro_name": "novobiocin", "category_aro_cvterm_id": "36250", "category_aro_accession": "3000111", "category_aro_class_name": "Antibiotic", "category_aro_description": "Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling."}, "40939": {"category_aro_name": "Clofazimine", "category_aro_cvterm_id": "40939", "category_aro_accession": "3004012", "category_aro_class_name": "Antibiotic", "category_aro_description": "Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death."}, "40938": {"category_aro_name": "clinafloxacin", "category_aro_cvterm_id": "40938", "category_aro_accession": "3004011", "category_aro_class_name": "Antibiotic", "category_aro_description": "Clinafloxacin is a fluoroquinolone antibiotic and gyrase (DNA topoisomerase II) inhibitor. It binds to DNA gyrase and disrupts replication by causing double-stranded DNA breaks, resulting in cell death."}, "36289": {"category_aro_name": "coumermycin A1", "category_aro_cvterm_id": "36289", "category_aro_accession": "3000150", "category_aro_class_name": "Antibiotic", "category_aro_description": "Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling."}, "35954": {"category_aro_name": "ciprofloxacin", "category_aro_cvterm_id": "35954", "category_aro_accession": "0000036", "category_aro_class_name": "Antibiotic", "category_aro_description": "Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome."}, "35997": {"category_aro_name": "antibiotic target alteration", "category_aro_cvterm_id": "35997", "category_aro_accession": "0001001", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance."}, "35920": {"category_aro_name": "fluoroquinolone antibiotic", "category_aro_cvterm_id": "35920", "category_aro_accession": "0000001", "category_aro_class_name": "Drug Class", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death."}, "40940": {"category_aro_name": "fleroxacin", "category_aro_cvterm_id": "40940", "category_aro_accession": "3004013", "category_aro_class_name": "Antibiotic", "category_aro_description": "Fleroxacin is a broad spectrum fluoroquinolone antibiotic that inhibits the DNA supercoiling activity of bacterial DNA gyrase, resulting in double-stranded DNA breaks and subsequent cell death."}, "40937": {"category_aro_name": "cinoxacin", "category_aro_cvterm_id": "40937", "category_aro_accession": "3004010", "category_aro_class_name": "Antibiotic", "category_aro_description": "Cinoxacin is a fluoroquinolone antibiotic primarily used for the treatment of urinary tract infections in adults. Cinoxacin binds to DNA gyrase, resulting in double-stranded DNA breaks and cell death."}}, "ARO_name": "Clostridium difficile gyrB conferring resistance to fluoroquinolone", "model_type": "protein variant model", "model_description": "The protein variant model is an AMR detection model. 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.", "ARO_id": "42469", "model_name": "Clostridium difficile gyrB conferring resistance to fluoroquinolone", "model_type_id": "40293"}}}