Halobacterium salinarum 16S rRNA mutation conferring resistance to pactamycin

Download Sequences
Accession ARO:3003977
CARD Short NameHsal_16S_PAC
DefinitionPoint mutations in Halobacterium 16S rRNA that confer resistance to pactamycin antibiotic.
AMR Gene Family16S rRNA with mutation conferring resistance to pactamycin
Drug Classpactamycin-like antibiotic
Resistance Mechanismantibiotic target alteration
Classification10 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic pactamycin [Antibiotic]
+ 16S rRNA with mutation conferring resistance to pactamycin [AMR Gene Family]
Publications

Mankin AS, et al. 1997. J. Mol. Biol. 274(1):8-15 Pactamycin resistance mutations in functional sites of 16 S rRNA. (PMID 9398510)
Resistomes

Prevalence of Halobacterium salinarum 16S rRNA mutation conferring resistance to pactamycin 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: rRNA gene variant model

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
No prevalence data


Detection Models

Model Type: rRNA gene variant model

Model Definition: Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA 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 BLASTN bit-score above the curated BLASTN 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 BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.

Bit-score Cut-off (blastN): 2600

PubMed: mutation data hand curated from the scientific literature, evaluated as conferring resistance (R). CRyPTIC: mutation data acquired from the CRyPTIC catalog, evaluated as resistant (R), susceptible (S), or undetermined (U). ReSeqTB: mutation data acquired from the ReSeqTB catalog, evaluated as conferring resistance (Minimal, Moderate, High), not conferring resistance (None), or Indeterminate. WHO: mutation data acquired from the WHO 2023 catalog, evaluated as resistant (R), susceptible (S), or undetermined (U).

MutationMutation typePubMed
a633gsingle resistance variantPMID:9398510
c734tsingle resistance variantPMID:9398510
c735tsingle resistance variantPMID:9398510


>gb|KY084523.1|+|1-1473|Halobacterium salinarum 16S rRNA mutation conferring resistance to pactamycin [Halobacterium salinarum]
ATTCCGGTTGATCCTGCCGGAGGCCATTGCTATCGGAGTCCGATTTAGCCATGCTAGTTGTGCGGGTTTAGACCCGCAGCGGAAAGCTCA
GTAACACGTGGCCAAGCTACCCTGTGGACGGGAATACTCTCGGGAAACTGAGGCTAATCCCCGATAACGCTTTGCTCCTGGAAGGGGCAA
AGCCGGAAACGCTCCGGCGCCACAGGATGCGGCTGCGGTCGCCTAGGTAGACGGTGGGGTAACGGCCCACCGTGCCCATAATCGGTACGG
GCCGTGAGCCCAAGAGCCCGGAGACGGAATCTGAGACAAGATTCCGGGCCCTACGGGGCGCAGCAGGCGCGAAACCTTTACACTGTACGA
AAGTGCGATAAGGGGACTCCGAGTGTGAAGGCATAGAGCCTTCACTTTTGTACACCGTAAGGTGGTGCACGAATAAGGACTGGGCAAGAC
CGGTGCCAGCCGCCGCGGTAATACCGGCAGTCCGAGTGATGGCCGATCTTATTGGGCCTAAAGCGTCCGTAGCTGGCTGAACAAGTCCGT
TGGGAAATCTGTCCGCTTAACGGGCAGGCGTCCAGCGGCCACTGTTCAGCTTGGGACCCCCCGACCTGAGGGGTACGTCTGGGGTAGGAG
TGAAATCCTGTAATCCTGGACGGACCGCCGGTGGCGAAAGCGCCTCAGGAGAACGGATCCGACAGTGAGGGACGAAAGCTAGGGTCTCGA
ACCGGATTAGATACCCGGGTAGTCCTAGCTGTAAACGATGTCCGCTAGGTGTGGCGCAGGCTACGAGCCTGCGCTGTGCCGTAGGGAAGC
CGAGAAGCGGACCGCCTGGGAAGTACGTCTGCAAGGATGAAACTTAAAGGAATTGGCGGGGGAGCACTACAACCGGAGGAGCCTGCGGTT
TAATTGGACTCAACGCCGGACATCTCACCAGCCCCGACAGTAGTAATGACGGTCAGGTTGATGACCTTACCCGAGGCTACTGAGAGGAGG
TGCATGGCCGCCGTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCGCACTCCTACCTGCCAGCAGTACCCTT
TGGGTAGCTGGGTACATTAGGTGGACTGCCGCTGCCAAAGCGGAGGAAGGAACGGGCAACGGTAGGTCAGTATGCCCCGAATGGGCTGGG
CAACACGCGGGCTACAATGGTCGAGACAATGGGAAGCCACTCCGAGAGGAGGCGCTAATCTCCTAAACTCGATCGTAGTTCGGATTGAGG
GCTGAAACTCGCCCTCATGAAGCTGGATTCGGTAGTAATCGCGTGTCAGCAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGC
CCGTCAAATCACCCGAGTGGGGTTCGGATGAGGCCGGCATGCGCTGGTCAAATCTGGGCTCCGCAAGGGGGATTAAGTCGTAACAAGGTA
GCCGTAGGGGAATCTGCGGCTGGATCACCTCCT

Curator Acknowledgements
Curator Description Most Recent Edit