basR

Accession ARO:3003582
Synonym(s)pmrA
DefinitionResponse regulator for Lipid A modification genes; two-component system involved in polymyxin resistance that senses high extracellular Fe(2+)
AMR Gene Familypmr phosphoethanolamine transferase
Drug Classpeptide antibiotic
Resistance Mechanismantibiotic target alteration
Classification14 ontology terms | Show
Parent Term(s)3 ontology terms | Show
Publications

Lean SS, et al. 2014. ISRN Microbiol 2014: 953417. Prevalence and Genetic Characterization of Carbapenem- and Polymyxin-Resistant Acinetobacter baumannii Isolated from a Tertiary Hospital in Terengganu, Malaysia. (PMID 25006521)

Resistomes

Prevalence of basR among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI for 82 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, 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 (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGS
Pseudomonas aeruginosa0%0%0%
Pseudomonas fluorescens3.7%0%0%
Show Perfect Only


Detection Models

Model Type: protein variant model

Model Definition: 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.

Legend:

  • discovered in clinical, agricultural, or environmental isolates
  • discovered via laboratory selection experiments


Bit-score Cut-off (blastP): 375

PMID in progress (single): L71R L157Q


>gb|AAG08162.1|+|basR [Pseudomonas aeruginosa PAO1]
MRILLAEDDLLLGDGIRAGLRLEGDTVEWVTDGVAAENALVTDEFDLLVLDIGLPRRSGL
DILRNLRHQGLLTPVLLLTARDKVADRVAGLDSGADDYLTKPFDLDELQARVRALTRRTT
GRALPQLVHGELRLDPATHQVTLSGQAVELAPREYALLRLLLENSGKVLSRNQLEQSLYG
WSGDVESNAIEVHVHHLRRKLGNQLIRTVRGIGYGIDQPAP



>gb|AE004091.2|+|5364071-5364736|basR [Pseudomonas aeruginosa PAO1]
ATGAGAATACTGCTGGCCGAGGACGACCTGCTGCTCGGCGACGGCATCCGCGCCGGGCTGCGCCTGGAAGGCGATACCGTGGAATGGGTG
ACCGACGGCGTGGCCGCGGAGAACGCGCTGGTCACCGACGAGTTCGACCTGCTGGTGCTCGACATCGGACTGCCGCGCCGCAGCGGCCTG
GACATCCTGCGCAACCTGCGTCACCAGGGCCTGCTCACCCCGGTGCTGCTGCTCACCGCGCGGGACAAGGTGGCCGACCGGGTCGCCGGG
CTCGACAGCGGTGCCGACGACTACCTGACCAAGCCCTTCGATCTCGACGAACTGCAGGCACGGGTGCGCGCCCTGACCCGCCGCACCACC
GGTCGCGCCCTGCCGCAACTGGTGCACGGCGAGCTGCGCCTGGACCCGGCGACCCACCAGGTGACCCTGTCCGGGCAGGCGGTGGAACTG
GCGCCGCGCGAATACGCACTGCTGCGCCTGCTGCTGGAGAACAGCGGCAAGGTGCTCTCGCGCAACCAACTGGAGCAGAGCCTCTACGGC
TGGAGCGGCGACGTCGAGAGCAACGCCATCGAAGTCCACGTCCACCACCTGCGGCGCAAGCTCGGCAACCAGTTGATCCGCACCGTCCGC
GGCATCGGCTACGGCATCGACCAGCCGGCGCCCTGA