Accession ARO:3003064
CARD Short NameykkD
DefinitionykkD is an SMR-type protein that is a subunit of the ykkCD efflux pump.
AMR Gene Familysmall multidrug resistance (SMR) antibiotic efflux pump
Drug Classphenicol antibiotic, tetracycline antibiotic, aminoglycoside antibiotic
Resistance Mechanismantibiotic efflux
Efflux Componentefflux pump complex or subunit conferring antibiotic resistance
Resistomes with Perfect MatchesBacillus subtilisg+wgs
Resistomes with Sequence VariantsBacillus halotoleransg+wgs, Bacillus subtilisg+wgs, Bacillus tequilensisg+wgs
Classification13 ontology terms | Show
Parent Term(s)2 ontology terms | Show

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).

Prevalence: protein homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Bacillus halotolerans100%0%89.19%0%
Bacillus subtilis97.49%0%78.61%0%
Bacillus tequilensis100%0%100%0%
Show Perfect Only

Detection Models

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

>gb|CAB13167.1|+|ykkD [Bacillus subtilis subsp. subtilis str. 168]

>gb|AL009126.1|+|1376855-1377172|ykkD [Bacillus subtilis subsp. subtilis str. 168]