APH(4)-Ia

Accession	ARO:3002655
Synonym(s)	hph
CARD Short Name	APH(4)-Ia
Definition	APH(4)-Ia is a plasmid-encoded aminoglycoside phosphotransferase in E. coli.
AMR Gene Family	APH(4)
Drug Class	aminoglycoside antibiotic
Resistance Mechanism	antibiotic inactivation
Resistomes with Perfect Matches	Acinetobacter baumannii^p+wgs, Acinetobacter johnsonii^wgs, Acinetobacter towneri^p+wgs, Citrobacter freundii^p+wgs, Citrobacter portucalensis^wgs, Citrobacter youngae^wgs, Enterobacter cloacae^wgs, Enterobacter hormaechei^wgs, Enterobacter roggenkampii^wgs, Escherichia albertii^wgs, Escherichia coli^g+p+wgs+gi, Escherichia fergusonii^p+wgs, Klebsiella michiganensis^p, Klebsiella oxytoca^p, Klebsiella pneumoniae^g+p+wgs+gi, Klebsiella quasipneumoniae^p+wgs, Morganella morganii^g+wgs+gi, Proteus columbae^g+gi, Proteus mirabilis^g+p+wgs+gi, Proteus penneri^wgs, Proteus vulgaris^p+wgs, Providencia alcalifaciens^g, Providencia rettgeri^g+p+wgs, Providencia stuartii^g+gi, Pseudomonas aeruginosa^p+wgs, Salmonella enterica^g+p+wgs+gi, Shigella flexneri^g+p, Shigella sonnei^wgs, Streptococcus suis^wgs
Resistomes with Sequence Variants	Acinetobacter baumannii^p+wgs, Acinetobacter johnsonii^wgs, Acinetobacter towneri^p+wgs, Bacillus subtilis^g, Citrobacter freundii^p+wgs, Citrobacter portucalensis^wgs, Citrobacter youngae^wgs, Enterobacter cloacae^wgs, Enterobacter hormaechei^wgs, Enterobacter roggenkampii^wgs, Escherichia albertii^wgs, Escherichia coli^g+p+wgs+gi, Escherichia fergusonii^p+wgs, Klebsiella michiganensis^p, Klebsiella oxytoca^p, Klebsiella pneumoniae^g+p+wgs+gi, Klebsiella quasipneumoniae^p+wgs, Listeria monocytogenes^wgs, Morganella morganii^g+wgs+gi, Proteus columbae^g+gi, Proteus mirabilis^g+p+wgs+gi, Proteus penneri^wgs, Proteus vulgaris^p+wgs, Providencia alcalifaciens^g, Providencia rettgeri^g+p+wgs, Providencia stuartii^g+gi, Pseudomonas aeruginosa^p+wgs, Salmonella enterica^g+p+wgs+gi, Shigella flexneri^g+p, Shigella sonnei^wgs, Streptococcus suis^wgs
Classification	11 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 + aminoglycoside phosphotransferase (APH) + aminoglycoside antibiotic [Drug Class] + APH(4) [AMR Gene Family]
Parent Term(s)	2 ontology terms \| Show + confers_resistance_to_antibiotic hygromycin B [Antibiotic] + APH(4)-I
Publications	Kaster KR, et al. 1983. Nucleic Acids Res 11(19): 6895-6911. Analysis of a bacterial hygromycin B resistance gene by transcriptional and translational fusions and by DNA sequencing. (PMID 6314265)

Resistomes

Prevalence of APH(4)-Ia 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%	0.05%	0.01%	0%	0%
Acinetobacter baumannii	0%	0.05%	0.03%	0%	0%
Acinetobacter johnsonii	0%	0%	1.82%	0%	0%
Acinetobacter johnsonii	0%	0%	1.82%	0%	0%
Acinetobacter towneri	0%	12.5%	3.85%	0%	0%
Acinetobacter towneri	0%	12.5%	3.85%	0%	0%
Bacillus subtilis	0.36%	0%	0%	0%	0%
Bacillus subtilis	0%	0%	0%	0%	0%
Citrobacter freundii	0%	0.31%	0.58%	0%	0%
Citrobacter freundii	0%	0.31%	0.58%	0%	0%
Citrobacter portucalensis	0%	0%	2.7%	0%	0%
Citrobacter portucalensis	0%	0%	2.7%	0%	0%
Citrobacter youngae	0%	0%	6.25%	0%	0%
Citrobacter youngae	0%	0%	6.25%	0%	0%
Enterobacter cloacae	0%	0%	0.96%	0%	0%
Enterobacter cloacae	0%	0%	0.96%	0%	0%
Enterobacter hormaechei	0%	0%	0.26%	0%	0%
Enterobacter hormaechei	0%	0%	0.26%	0%	0%
Enterobacter roggenkampii	0%	0%	0.72%	0%	0%
Enterobacter roggenkampii	0%	0%	0.36%	0%	0%
Escherichia albertii	0%	0%	0.65%	0%	0%
Escherichia albertii	0%	0%	0.65%	0%	0%
Escherichia coli	0.24%	0.49%	2.69%	0.51%	0.22%
Escherichia coli	0.24%	0.49%	2.74%	0.51%	0.22%
Escherichia fergusonii	0%	2.85%	17.39%	0%	0%
Escherichia fergusonii	0%	2.85%	17.39%	0%	0%
Klebsiella michiganensis	0%	0.57%	0%	0%	0%
Klebsiella michiganensis	0%	0.57%	0%	0%	0%
Klebsiella oxytoca	0%	1.37%	0%	0%	0%
Klebsiella oxytoca	0%	1.37%	0%	0%	0%
Klebsiella pneumoniae	1.01%	0.68%	2.56%	1.9%	0%
Klebsiella pneumoniae	0.95%	0.67%	2.52%	1.9%	0%
Klebsiella quasipneumoniae	0%	0.85%	3.82%	0%	0%
Klebsiella quasipneumoniae	0%	0.85%	3.82%	0%	0%
Listeria monocytogenes	0%	0%	0%	0%	0%
Listeria monocytogenes	0%	0%	0.02%	0%	0%
Morganella morganii	11.54%	0%	7.98%	15.38%	0%
Morganella morganii	11.54%	0%	7.36%	15.38%	0%
Proteus columbae	100%	0%	0%	50%	0%
Proteus columbae	100%	0%	0%	50%	0%
Proteus mirabilis	28.44%	2.5%	21.29%	22.22%	0%
Proteus mirabilis	33.94%	2.5%	22.77%	25.93%	0%
Proteus penneri	0%	0%	25%	0%	0%
Proteus penneri	0%	0%	25%	0%	0%
Proteus vulgaris	0%	11.11%	5.56%	0%	0%
Proteus vulgaris	0%	11.11%	5.56%	0%	0%
Providencia alcalifaciens	9.09%	0%	0%	0%	0%
Providencia alcalifaciens	18.18%	0%	0%	0%	0%
Providencia rettgeri	5.88%	5.41%	7.64%	0%	0%
Providencia rettgeri	5.88%	5.41%	7.64%	0%	0%
Providencia stuartii	6.25%	0%	0%	33.33%	0%
Providencia stuartii	6.25%	0%	0%	33.33%	0%
Pseudomonas aeruginosa	0%	0.29%	0.09%	0%	0%
Pseudomonas aeruginosa	0%	0.29%	0.09%	0%	0%
Salmonella enterica	1.07%	5.2%	3.49%	2.32%	0%
Salmonella enterica	1.01%	5.14%	3.41%	2.32%	0%
Shigella flexneri	1%	0.8%	0%	0%	0%
Shigella flexneri	1%	0.8%	0%	0%	0%
Shigella sonnei	0%	0%	0.15%	0%	0%
Shigella sonnei	0%	0%	0.15%	0%	0%
Streptococcus suis	0%	0%	0.05%	0%	0%
Streptococcus suis	0%	0%	0.05%	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): 600

Protein
DNA

>gb|CAA24743.1|+|APH(4)-Ia [Escherichia coli]
MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGYVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYC
ISRRAQGVTLQDLPETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQTVMDDTVSASVAQALDE
LMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFGDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIG
LDQLYQSLVDGNFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE

>gb|V01499.1|+|231-1256|APH(4)-Ia [Escherichia coli]
ATGAAAAAGCCTGAACTCACCGCGACGTCTGTCGAGAAGTTTCTGATCGAAAAGTTCGACAGCGTCTCCGACCTGATGCAGCTCTCGGAG
GGCGAAGAATCTCGTGCTTTCAGCTTCGATGTAGGAGGGCGTGGATATGTCCTGCGGGTAAATAGCTGCGCCGATGGTTTCTACAAAGAT
CGTTATGTTTATCGGCACTTTGCATCGGCCGCGCTCCCGATTCCGGAAGTGCTTGACATTGGGGAATTCAGCGAGAGCCTGACCTATTGC
ATCTCCCGCCGTGCACAGGGTGTCACGTTGCAAGACCTGCCTGAAACCGAACTGCCCGCTGTTCTGCAGCCGGTCGCGGAGGCCATGGAT
GCGATCGCTGCGGCCGATCTTAGCCAGACGAGCGGGTTCGGCCCATTCGGACCGCAAGGAATCGGTCAATACACTACATGGCGTGATTTC
ATATGCGCGATTGCTGATCCCCATGTGTATCACTGGCAAACTGTGATGGACGACACCGTCAGTGCGTCCGTCGCGCAGGCTCTCGATGAG
CTGATGCTTTGGGCCGAGGACTGCCCCGAAGTCCGGCACCTCGTGCACGCGGATTTCGGCTCCAACAATGTCCTGACGGACAATGGCCGC
ATAACAGCGGTCATTGACTGGAGCGAGGCGATGTTCGGGGATTCCCAATACGAGGTCGCCAACATCTTCTTCTGGAGGCCGTGGTTGGCT
TGTATGGAGCAGCAGACGCGCTACTTCGAGCGGAGGCATCCGGAGCTTGCAGGATCGCCGCGGCTCCGGGCGTATATGCTCCGCATTGGT
CTTGACCAACTCTATCAGAGCTTGGTTGACGGCAATTTCGATGATGCAGCTTGGGCGCAGGGTCGATGCGACGCAATCGTCCGATCCGGA
GCCGGGACTGTCGGGCGTACACAAATCGCCCGCAGAAGCGCGGCCGTCTGGACCGATGGCTGTGTAGAAGTACTCGCCGATAGTGGAAAC
CGACGCCCCAGCACTCGTCCGAGGGCAAAGGAATAG

Curator Acknowledgements

Curator	Description	Most Recent Edit

APH(4)-Ia

Prevalence: protein homolog model (view sequences)

Graph