| Accession | ARO:3003064 |
| CARD Short Name | ykkD |
| Definition | ykkD is an SMR-type protein that is a subunit of the ykkCD efflux pump. |
| AMR Gene Family | small multidrug resistance (SMR) antibiotic efflux pump |
| Drug Class | phenicol antibiotic, tetracycline antibiotic, aminoglycoside antibiotic |
| Resistance Mechanism | antibiotic efflux |
| Efflux Component | efflux pump complex or subunit conferring antibiotic resistance |
| Resistomes with Perfect Matches | Bacillus subtilisg+wgs |
| Resistomes with Sequence Variants | Bacillus halotoleransg+wgs, Bacillus subtilisg+wgs, Bacillus tequilensisg+wgs |
| 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] + phenicol antibiotic [Drug Class] + efflux pump complex or subunit conferring antibiotic resistance [Efflux Component] + tetracycline antibiotic [Drug Class] + aminoglycoside antibiotic [Drug Class] + chloramphenicol [Antibiotic] + small multidrug resistance (SMR) antibiotic efflux pump [AMR Gene Family] + tetracycline [Antibiotic] + streptomycin [Antibiotic] |
| Parent Term(s) | 2 ontology terms | Show |
| Publications | Jack DL, et al. 2000. J Bacteriol 182(8): 2311-2313. A broad-specificity multidrug efflux pump requiring a pair of homologous SMR-type proteins. (PMID 10735877) |
Prevalence of ykkD 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 |
|---|---|---|---|---|
| Bacillus halotolerans | 100% | 0% | 89.19% | 0% |
| Bacillus subtilis | 97.49% | 0% | 78.61% | 0% |
| Bacillus tequilensis | 100% | 0% | 100% | 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): 180