| Ontology | CARD's Antibiotic Resistance Ontology |
| Accession | ARO:3000024 |
| CARD Short Name | patA |
| Definition | PatA is an ABC transporter of Streptococcus pneumoniae that interacts with PatB to confer fluoroquinolone resistance. |
| AMR Gene Family | ATP-binding cassette (ABC) antibiotic efflux pump |
| Drug Class | fluoroquinolone antibiotic |
| Resistance Mechanism | antibiotic efflux |
| Efflux Component | efflux pump complex or subunit conferring antibiotic resistance |
| Resistomes with Perfect Matches | Streptococcus pneumoniaeg+wgs |
| Resistomes with Sequence Variants | Streptococcus cristatusg+wgs, Streptococcus gordoniig+wgs, Streptococcus gwangjuenseg+wgs, Streptococcus mitisg+wgs, Streptococcus pneumoniaeg+wgs, Streptococcus pseudopneumoniaeg+wgs, Streptococcus sanguinisg+wgs |
| Classification | 10 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + determinant of antibiotic resistance + antibiotic molecule + antibiotic efflux [Resistance Mechanism] + efflux pump complex or subunit conferring antibiotic resistance [Efflux Component] + fluoroquinolone antibiotic [Drug Class] + norfloxacin [Antibiotic] + ATP-binding cassette (ABC) antibiotic efflux pump [AMR Gene Family] + ciprofloxacin [Antibiotic] |
| Parent Term(s) | 2 ontology terms | Show |
| Publications | El Garch F, et al. 2010. J Antimicrob Chemother 65(10): 2076-2082. Fluoroquinolones induce the expression of patA and patB, which encode ABC efflux pumps in Streptococcus pneumoniae. (PMID 20709735) Garvey MI, et al. 2010. Antimicrob Agents Chemother 55(1): 190-196. Overexpression of patA and patB, which encode ABC transporters, is associated with fluoroquinolone resistance in clinical isolates of Streptococcus pneumoniae. (PMID 20937787) |
Prevalence of patA 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).
| Species | NCBI Chromosome | NCBI Plasmid | NCBI WGS | NCBI GI | GRDI-AMR2 |
|---|---|---|---|---|---|
| Streptococcus cristatus | 100% | 0% | 100% | 0% | 0% |
| Streptococcus gordonii | 100% | 0% | 98.72% | 0% | 0% |
| Streptococcus gwangjuense | 100% | 0% | 100% | 0% | 0% |
| Streptococcus mitis | 100% | 0% | 98.99% | 0% | 0% |
| Streptococcus pneumoniae | 99.51% | 0% | 98.44% | 0% | 0% |
| Streptococcus pseudopneumoniae | 100% | 0% | 99.15% | 0% | 0% |
| Streptococcus sanguinis | 100% | 0% | 100% | 0% | 0% |
Model Type: protein homolog model
Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
Bit-score Cut-off (blastP): 750
| Curator | Description | Most Recent Edit |
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