Mycobacterium tuberculosis gpsI with mutations conferring resistance to pyrazinamide

Accession ARO:3004977
Synonym(s)Rv2783c
CARD Short NameMtub_gpsI_PZA
DefinitionMutations in gpsI that can contribute to or confer resistance to pyrazinamide.
AMR Gene Familypyrazinamide resistant gpsI
Drug Classpyrazine antibiotic
Resistance Mechanismantibiotic target alteration
Classification9 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic pyrazinamide [Antibiotic]
+ pyrazinamide resistant gpsI [AMR Gene Family]
Publications

Sheen P, et al. 2017. BMC Genomics 18(1):769 A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. (PMID 29020922)

Ezewudo M, et al. 2018. Sci Rep 8(1):15382 Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. (PMID 30337678)

Resistomes

Prevalence of Mycobacterium tuberculosis gpsI with mutations conferring resistance to pyrazinamide among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 414 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: protein variant model

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
No prevalence data


Detection Models

Model Type: protein variant model

Model Definition: Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.

Bit-score Cut-off (blastP): 1400


>gb|NP_217299.1|-|Mycobacterium tuberculosis gpsI with mutations conferring resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv]
MSAAEIDEGVFETTATIDNGSFGTRTIRFETGRLALQAAGAVVAYLDDDNMLLSATTASKNPKEHFDFFPLTVDVEERMYAAGRIPGSFF
RREGRPSTDAILTCRLIDRPLRPSFVDGLRNEIQIVVTILSLDPGDLYDVLAINAASASTQLGGLPFSGPIGGVRVALIDGTWVGFPTVD
QIERAVFDMVVAGRIVEGDVAIMMVEAEATENVVELVEGGAQAPTESVVAAGLEAAKPFIAALCTAQQELADAAGKSGKPTVDFPVFPDY
GEDVYYSVSSVATDELAAALTIGGKAERDQRIDEIKTQVVQRLADTYEGREKEVGAALRALTKKLVRQRILTDHFRIDGRGITDIRALSA
EVAVVPRAHGSALFERGETQILGVTTLDMIKMAQQIDSLGPETSKRYMHHYNFPPFSTGETGRVGSPKRREIGHGALAERALVPVLPSVE
EFPYAIRQVSEALGSNGSTSMGSVCASTLALLNAGVPLKAPVAGIAMGLVSDDIQVEGAVDGVVERRFVTLTDILGAEDAFGDMDFKVAG
TKDFVTALQLDTKLDGIPSQVLAGALEQAKDARLTILEVMAEAIDRPDEMSPYAPRVTTIKVPVDKIGEVIGPKGKVINAITEETGAQIS
IEDDGTVFVGATDGPSAQAAIDKINAIANPQLPTVGERFLGTVVKTTDFGAFVSLLPGRDGLVHISKLGKGKRIAKVEDVVNVGDKLRVE
IADIDKRGKISLILVADEDSTAAATDAATVTS


>gb|NC_000962.3|-|3090339-3092597|Mycobacterium tuberculosis gpsI with mutations conferring resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv]
ATGTCTGCCGCTGAAATTGACGAAGGCGTGTTCGAGACGACCGCCACCATCGACAACGGGAGCTTTGGCACCCGGACCATCCGCTTCGAG
ACCGGCCGATTGGCCTTGCAGGCCGCCGGCGCGGTGGTCGCCTACCTCGACGACGACAACATGCTGCTGTCGGCGACCACCGCCAGCAAG
AACCCCAAAGAACACTTCGACTTCTTCCCCCTCACGGTCGACGTCGAGGAGCGCATGTATGCGGCCGGCCGCATCCCCGGTTCGTTCTTC
CGTCGCGAGGGCCGACCCTCCACCGACGCGATCCTGACCTGCCGGCTCATCGACCGCCCGCTGCGCCCGTCGTTTGTCGACGGGCTGCGC
AACGAGATCCAAATCGTGGTGACGATTCTCAGCCTGGATCCGGGCGATCTCTACGACGTATTGGCGATCAACGCGGCGTCGGCGTCCACC
CAGCTGGGCGGTCTGCCGTTCTCCGGGCCCATCGGCGGTGTGCGGGTGGCGCTCATCGACGGCACCTGGGTCGGCTTCCCCACCGTCGAC
CAGATCGAGCGCGCCGTGTTCGACATGGTCGTGGCCGGCCGGATCGTCGAGGGTGATGTTGCCATCATGATGGTCGAAGCCGAGGCCACC
GAAAACGTCGTCGAGCTCGTCGAAGGTGGTGCCCAAGCGCCGACGGAAAGCGTGGTGGCCGCGGGCCTGGAGGCGGCCAAGCCGTTTATC
GCCGCGCTGTGCACCGCGCAGCAGGAGCTTGCCGATGCCGCTGGAAAGTCGGGCAAACCGACCGTCGACTTCCCGGTGTTCCCTGACTAC
GGCGAAGACGTGTACTACTCGGTGTCCTCGGTGGCCACCGACGAGTTGGCCGCCGCGTTGACCATCGGCGGTAAAGCCGAGCGCGACCAG
CGCATCGACGAAATCAAGACCCAGGTTGTGCAGCGGCTCGCCGACACCTACGAGGGTCGCGAAAAGGAGGTCGGCGCCGCGTTGCGTGCC
CTGACCAAAAAGCTGGTTCGGCAGCGCATCCTCACCGACCATTTCCGTATCGACGGCCGCGGCATCACCGACATTCGCGCATTGTCGGCC
GAGGTGGCCGTGGTTCCGCGCGCGCACGGCAGCGCGCTGTTCGAACGCGGCGAAACCCAGATCCTGGGTGTGACCACACTCGACATGATC
AAGATGGCCCAGCAGATCGACTCGTTGGGGCCGGAGACATCGAAGCGGTACATGCACCACTACAACTTCCCGCCGTTCTCCACCGGCGAG
ACCGGTCGGGTCGGTTCGCCCAAGCGGCGTGAGATCGGGCACGGCGCACTGGCCGAGCGGGCCCTGGTGCCGGTGTTGCCGAGCGTCGAG
GAATTCCCGTATGCCATTCGCCAGGTGTCGGAGGCTCTGGGCTCCAACGGGTCGACCTCGATGGGGTCGGTGTGCGCGTCGACGCTGGCG
CTGCTCAACGCCGGGGTGCCGCTCAAGGCGCCGGTGGCCGGCATCGCGATGGGCCTGGTCTCCGACGACATTCAAGTAGAAGGGGCGGTC
GACGGCGTTGTGGAGCGTCGCTTCGTCACCCTCACCGACATCCTCGGCGCCGAAGACGCGTTCGGTGACATGGACTTCAAGGTCGCCGGG
ACCAAGGACTTCGTCACCGCGCTGCAGCTGGACACCAAGCTCGACGGGATCCCTTCGCAGGTGCTTGCCGGAGCACTCGAGCAGGCCAAG
GACGCCCGCCTCACGATCTTGGAGGTGATGGCTGAGGCCATCGATAGACCCGACGAAATGAGTCCCTACGCCCCGCGGGTGACCACCATC
AAGGTTCCGGTGGACAAGATCGGGGAGGTCATCGGACCCAAGGGCAAGGTCATCAACGCCATCACCGAGGAGACCGGCGCGCAGATCTCC
ATCGAAGACGACGGCACCGTGTTCGTCGGCGCCACCGACGGGCCATCGGCACAGGCCGCGATCGACAAGATCAACGCCATCGCCAACCCG
CAGCTGCCGACGGTGGGCGAACGGTTCCTCGGAACCGTGGTCAAGACCACCGATTTCGGTGCCTTTGTATCGTTGCTGCCTGGCCGCGAC
GGTCTGGTGCACATTTCCAAACTCGGCAAGGGCAAGCGCATCGCGAAGGTCGAGGACGTTGTCAATGTCGGTGACAAGCTGCGGGTGGAG
ATCGCCGACATCGACAAACGGGGCAAGATCTCCCTGATCCTGGTCGCCGACGAGGACAGCACCGCCGCCGCTACCGATGCCGCGACGGTC
ACCAGCTGA

Curator Acknowledgements
Curator Description Most Recent Edit