APH(3')-IIa

Accession	ARO:3002644
Synonym(s)	aphA-2
CARD Short Name	APH(3')-IIa
Definition	APH(3')-IIa is a transposon-encoded aminoglycoside phosphotransferase in E. coli.
AMR Gene Family	APH(3')
Drug Class	aminoglycoside antibiotic
Resistance Mechanism	antibiotic inactivation
Resistomes with Perfect Matches	Acinetobacter baumannii^wgs, Acinetobacter johnsonii^wgs, Acinetobacter lwoffii^wgs, Burkholderia glumae^g, Clostridium botulinum^wgs, Corynebacterium pseudotuberculosis^g, Elizabethkingia anophelis^wgs, Enterobacter asburiae^g, Enterobacter cloacae^wgs, Enterobacter hormaechei^wgs, Escherichia albertii^p, Escherichia coli^g+p+wgs, Escherichia fergusonii^p+wgs, Klebsiella michiganensis^wgs, Klebsiella oxytoca^p, Klebsiella pneumoniae^g+p+wgs, Klebsiella quasipneumoniae^wgs, Leptospira interrogans^wgs, Listeria monocytogenes^wgs, Phocaeicola dorei^wgs, Proteus mirabilis^wgs, Pseudomonas aeruginosa^g+wgs, Pseudomonas putida^g+wgs, Rhizobium leguminosarum^wgs, Salmonella enterica^g+p+wgs, Serratia marcescens^wgs, Shigella flexneri^p, Shigella sonnei^wgs, Staphylococcus aureus^wgs, Staphylococcus epidermidis^wgs, Streptococcus suis^wgs
Resistomes with Sequence Variants	Acinetobacter baumannii^wgs, Acinetobacter johnsonii^wgs, Acinetobacter lwoffii^wgs, Aeromonas caviae^wgs, Burkholderia glumae^g, Burkholderia multivorans^wgs, Clostridium botulinum^wgs, Corynebacterium pseudotuberculosis^g, Elizabethkingia anophelis^wgs, Enterobacter asburiae^g, Enterobacter cloacae^wgs, Enterobacter hormaechei^wgs, Escherichia albertii^p, Escherichia coli^g+p+wgs, Escherichia fergusonii^p+wgs, Klebsiella michiganensis^wgs, Klebsiella oxytoca^p, Klebsiella pneumoniae^g+p+wgs, Klebsiella quasipneumoniae^wgs, Leptospira interrogans^wgs, Listeria monocytogenes^wgs, Phocaeicola dorei^wgs, Proteus mirabilis^wgs, Pseudomonas aeruginosa^g+p+wgs, Pseudomonas putida^g+wgs, Rhizobium leguminosarum^wgs, Rhodopseudomonas palustris^g, Salmonella enterica^g+p+wgs, Serratia marcescens^wgs, Shigella flexneri^p, Shigella sonnei^wgs, Staphylococcus aureus^wgs, Staphylococcus epidermidis^wgs, Stenotrophomonas maltophilia^wgs, Streptococcus suis^wgs, Vibrio cholerae^g, Xanthomonas oryzae^g
Classification	13 ontology terms \| Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + determinant of antibiotic resistance + antibiotic inactivation [Resistance Mechanism] + antibiotic inactivation enzyme + aminoglycoside modifying enzyme + phosphorylation of antibiotic conferring resistance + antibiotic molecule + antibiotic mixture + aminoglycoside phosphotransferase (APH) + aminoglycoside antibiotic [Drug Class] + gentamicin [Antibiotic] + APH(3') [AMR Gene Family]
Parent Term(s)	7 ontology terms \| Show + confers_resistance_to_antibiotic neomycin [Antibiotic] + confers_resistance_to_antibiotic ribostamycin [Antibiotic] + confers_resistance_to_antibiotic butirosin [Antibiotic] + confers_resistance_to_antibiotic kanamycin A [Antibiotic] + confers_resistance_to_antibiotic gentamicin B [Antibiotic] + confers_resistance_to_antibiotic paromomycin [Antibiotic] + APH(3')-II
Publications	Beck E, et al. 1982. Gene 19(3): 327-336. Nucleotide sequence and exact localization of the neomycin phosphotransferase gene from transposon Tn5. (PMID 6295884)

Resistomes

Prevalence of APH(3')-IIa 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).

Prevalence: protein homolog model (view sequences)

Species	NCBI Chromosome	NCBI Plasmid	NCBI WGS	NCBI GI	GRDI-AMR2
Acinetobacter baumannii	0%	0%	0.01%	0%	0%
Acinetobacter baumannii	0%	0%	0.06%	0%	0%
Acinetobacter johnsonii	0%	0%	1.82%	0%	0%
Acinetobacter johnsonii	0%	0%	1.82%	0%	0%
Acinetobacter lwoffii	0%	0%	2.63%	0%	0%
Acinetobacter lwoffii	0%	0%	2.63%	0%	0%
Aeromonas caviae	0%	0%	0.54%	0%	0%
Aeromonas caviae	0%	0%	0%	0%	0%
Burkholderia glumae	8%	0%	0%	0%	0%
Burkholderia glumae	8%	0%	0%	0%	0%
Burkholderia multivorans	0%	0%	0.24%	0%	0%
Burkholderia multivorans	0%	0%	0%	0%	0%
Clostridium botulinum	0%	0%	0.54%	0%	0%
Clostridium botulinum	0%	0%	0.54%	0%	0%
Corynebacterium pseudotuberculosis	3.8%	0%	0%	0%	0%
Corynebacterium pseudotuberculosis	3.8%	0%	0%	0%	0%
Elizabethkingia anophelis	0%	0%	1.03%	0%	0%
Elizabethkingia anophelis	0%	0%	1.03%	0%	0%
Enterobacter asburiae	3.23%	0%	0%	0%	0%
Enterobacter asburiae	3.23%	0%	0%	0%	0%
Enterobacter cloacae	0%	0%	0.64%	0%	0%
Enterobacter cloacae	0%	0%	0.64%	0%	0%
Enterobacter hormaechei	0%	0%	0.22%	0%	0%
Enterobacter hormaechei	0%	0%	0.22%	0%	0%
Escherichia albertii	0%	0.56%	0%	0%	0%
Escherichia albertii	0%	0.56%	0%	0%	0%
Escherichia coli	0.24%	0.31%	2.2%	0%	1.29%
Escherichia coli	0.17%	0.3%	2.11%	0%	1.24%
Escherichia fergusonii	0%	2.14%	1.09%	0%	0%
Escherichia fergusonii	0%	2.14%	1.09%	0%	0%
Klebsiella michiganensis	0%	0%	0.53%	0%	0%
Klebsiella michiganensis	0%	0%	0.53%	0%	0%
Klebsiella oxytoca	0%	0.68%	0%	0%	0%
Klebsiella oxytoca	0%	0.68%	0%	0%	0%
Klebsiella pneumoniae	0.06%	0.13%	0.37%	0%	0%
Klebsiella pneumoniae	0.06%	0.15%	0.41%	0%	0%
Klebsiella quasipneumoniae	0%	0%	0.26%	0%	0%
Klebsiella quasipneumoniae	0%	0%	0.13%	0%	0%
Leptospira interrogans	0%	0%	0.65%	0%	0%
Leptospira interrogans	0%	0%	1.61%	0%	0%
Listeria monocytogenes	0%	0%	0.02%	0%	0%
Listeria monocytogenes	0%	0%	0.02%	0%	0%
Phocaeicola dorei	0%	0%	1.04%	0%	0%
Phocaeicola dorei	0%	0%	1.04%	0%	0%
Proteus mirabilis	0%	0%	0.17%	0%	0%
Proteus mirabilis	0%	0%	0.17%	0%	0%
Pseudomonas aeruginosa	0.31%	0.29%	0.9%	0%	0%
Pseudomonas aeruginosa	0.15%	0%	0.41%	0%	0%
Pseudomonas putida	1.41%	0%	0.53%	0%	0%
Pseudomonas putida	1.41%	0%	0.53%	0%	0%
Rhizobium leguminosarum	0%	0%	0.2%	0%	0%
Rhizobium leguminosarum	0%	0%	0.2%	0%	0%
Rhodopseudomonas palustris	0%	0%	0%	0%	0%
Rhodopseudomonas palustris	7.69%	0%	0%	0%	0%
Salmonella enterica	0.44%	1.59%	0.78%	0%	0%
Salmonella enterica	0.25%	1.53%	0.78%	0%	0%
Serratia marcescens	0%	0%	0.13%	0%	0%
Serratia marcescens	0%	0%	0.13%	0%	0%
Shigella flexneri	0%	0.4%	0%	0%	0%
Shigella flexneri	0%	0.4%	0%	0%	0%
Shigella sonnei	0%	0%	0.44%	0%	0%
Shigella sonnei	0%	0%	0.44%	0%	0%
Staphylococcus aureus	0%	0%	0.03%	0%	0%
Staphylococcus aureus	0%	0%	0.03%	0%	0%
Staphylococcus epidermidis	0%	0%	0.08%	0%	0%
Staphylococcus epidermidis	0%	0%	0.17%	0%	0%
Stenotrophomonas maltophilia	0%	0%	0%	0%	0%
Stenotrophomonas maltophilia	0%	0%	0.15%	0%	0%
Streptococcus suis	0%	0%	0.1%	0%	0%
Streptococcus suis	0%	0%	0.1%	0%	0%
Vibrio cholerae	0%	0%	0%	0%	0%
Vibrio cholerae	0.45%	0%	0%	0%	0%
Xanthomonas oryzae	0%	0%	0%	0%	0%
Xanthomonas oryzae	0.62%	0%	0%	0%	0%

Show Perfect Only

Detection Models

protein homolog model

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): 500

Protein
DNA

>gb|CAA23892.1|+|APH(3')-IIa [Escherichia coli]
MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRD
WLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPD
GEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF

>gb|V00618.1|+|151-945|APH(3')-IIa [Escherichia coli]
ATGATTGAACAAGATGGATTGCACGCAGGTTCTCCGGCCGCTTGGGTGGAGAGGCTATTCGGCTATGACTGGGCACAACAGACAATCGGC
TGCTCTGATGCCGCCGTGTTCCGGCTGTCAGCGCAGGGGCGCCCGGTTCTTTTTGTCAAGACCGACCTGTCCGGTGCCCTGAATGAACTG
CAGGACGAGGCAGCGCGGCTATCGTGGCTGGCCACGACGGGCGTTCCTTGCGCAGCTGTGCTCGACGTTGTCACTGAAGCGGGAAGGGAC
TGGCTGCTATTGGGCGAAGTGCCGGGGCAGGATCTCCTGTCATCTCACCTTGCTCCTGCCGAGAAAGTATCCATCATGGCTGATGCAATG
CGGCGGCTGCATACGCTTGATCCGGCTACCTGCCCATTCGACCACCAAGCGAAACATCGCATCGAGCGAGCACGTACTCGGATGGAAGCC
GGTCTTGTCGATCAGGATGATCTGGACGAAGAGCATCAGGGGCTCGCGCCAGCCGAACTGTTCGCCAGGCTCAAGGCGCGCATGCCCGAC
GGCGAGGATCTCGTCGTGACCCATGGCGATGCCTGCTTGCCGAATATCATGGTGGAAAATGGCCGCTTTTCTGGATTCATCGACTGTGGC
CGGCTGGGTGTGGCGGACCGCTATCAGGACATAGCGTTGGCTACCCGTGATATTGCTGAAGAGCTTGGCGGCGAATGGGCTGACCGCTTC
CTCGTGCTTTACGGTATCGCCGCTCCCGATTCGCAGCGCATCGCCTTCTATCGCCTTCTTGACGAGTTCTTCTGA

Curator Acknowledgements

Curator	Description	Most Recent Edit

APH(3')-IIa

Prevalence: protein homolog model (view sequences)

Graph