| Accession | ARO:3000809 |
| Synonym(s) | ompD |
| CARD Short Name | OpmD |
| Definition | OpmD is the outer membrane channel protein of the efflux complex MexGHI-OpmD. |
| AMR Gene Family | resistance-nodulation-cell division (RND) antibiotic efflux pump |
| Drug Class | tetracycline antibiotic, disinfecting agents and antiseptics, fluoroquinolone antibiotic |
| Resistance Mechanism | antibiotic efflux |
| Efflux Component | efflux pump complex or subunit conferring antibiotic resistance |
| Resistomes with Perfect Matches | Pseudomonas aeruginosag+wgs, Pseudomonas fluorescensg |
| Resistomes with Sequence Variants | Pseudomonas aeruginosag+wgs, Pseudomonas fluorescensg |
| Classification | 13 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] + tetracycline antibiotic [Drug Class] + disinfecting agents and antiseptics [Drug Class] + efflux pump complex or subunit conferring antibiotic resistance [Efflux Component] + fluoroquinolone antibiotic [Drug Class] + tetracycline [Antibiotic] + acriflavine [Antibiotic] + norfloxacin [Antibiotic] + resistance-nodulation-cell division (RND) antibiotic efflux pump [AMR Gene Family] |
| Parent Term(s) | 2 ontology terms | Show |
| Publications | Schweizer HP. 2003. Genet Mol Res 2(1): 48-62. Efflux as a mechanism of resistance to antimicrobials in Pseudomonas aeruginosa and related bacteria: unanswered questions. (PMID 12917802) Aendekerk S, et al. 2005. Microbiology 151(PT 4): 1113-1125. The MexGHI-OpmD multidrug efflux pump controls growth, antibiotic susceptibility and virulence in Pseudomonas aeruginosa via 4-quinolone-dependent cell-to-cell communication. (PMID 15817779) Aendekerk S, et al. 2002. Microbiology (Reading, Engl.) 148(Pt 8):2371-81 Characterization of a new efflux pump, MexGHI-OpmD, from Pseudomonas aeruginosa that confers resistance to vanadium. (PMID 12177331) Sekiya H, et al. 2003. Antimicrob. Agents Chemother. 47(9):2990-2 Functional cloning and characterization of a multidrug efflux pump, mexHI-opmD, from a Pseudomonas aeruginosa mutant. (PMID 12937010) |
Prevalence of OpmD among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 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 |
|---|---|---|---|---|
| Pseudomonas aeruginosa | 96.17% | 0% | 65.54% | 0% |
| Pseudomonas fluorescens | 2.78% | 0% | 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): 920