APH(2'')-If

Download Sequences

Accession	ARO:3004191
CARD Short Name	APH(2'')-If
Definition	Aminoglycoside 2''-phosphotransferase identified from the gram-negative pathogen Campylobacter jejuni. APH(2'')-If was shown to confer resistance to 4,6-disubstituted antibiotics kanamycin, tobramycin, dibekacin, gentamicin and sisomicin through antibiotic phosphorylation. Described by Toth et al. 2013.
AMR Gene Family	APH(2'')
Drug Class	aminoglycoside antibiotic
Resistance Mechanism	antibiotic inactivation
Resistomes with Perfect Matches	Actinobacillus indolicus^g, Campylobacter coli^g+p+wgs, Campylobacter jejuni^g+p+wgs, Campylobacter upsaliensis^wgs, Helicobacter pullorum^wgs, Streptococcus suis^wgs
Resistomes with Sequence Variants	Actinobacillus indolicus^g, Campylobacter coli^g+p+wgs, Campylobacter jejuni^g+p+wgs, Campylobacter upsaliensis^wgs, Faecalibacterium prausnitzii^wgs, Helicobacter pullorum^wgs, Ruthenibacterium lactatiformans^wgs, Streptococcus suis^wgs
Classification	12 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 + antibiotic molecule + aminoglycoside modifying enzyme + antibiotic mixture + phosphorylation of antibiotic conferring resistance + aminoglycoside antibiotic [Drug Class] + gentamicin [Antibiotic] + aminoglycoside phosphotransferase (APH)
Parent Term(s)	6 ontology terms \| Show + confers_resistance_to_antibiotic dibekacin [Antibiotic] + confers_resistance_to_antibiotic sisomicin [Antibiotic] + confers_resistance_to_antibiotic kanamycin A [Antibiotic] + confers_resistance_to_antibiotic tobramycin [Antibiotic] + APH(2'') [AMR Gene Family] + confers_resistance_to_antibiotic gentamicin A [Antibiotic]
Publications	Toth M, et al. 2013. Antimicrob. Agents Chemother. 57(1):452-7 Novel aminoglycoside 2''-phosphotransferase identified in a gram-negative pathogen. (PMID 23129050)

Resistomes

Prevalence of APH(2'')-If 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
Actinobacillus indolicus	100%	0%	0%	0%	0%
Actinobacillus indolicus	100%	0%	0%	0%	0%
Campylobacter coli	4.35%	0.91%	2.73%	0%	0%
Campylobacter coli	8.7%	0.91%	6.42%	0%	0%
Campylobacter jejuni	3.86%	0.99%	1.23%	0%	0%
Campylobacter jejuni	5.26%	3.96%	2.65%	0%	0%
Campylobacter upsaliensis	0%	0%	16.8%	0%	0%
Campylobacter upsaliensis	0%	0%	12%	0%	0%
Faecalibacterium prausnitzii	0%	0%	0.97%	0%	0%
Faecalibacterium prausnitzii	0%	0%	0%	0%	0%
Helicobacter pullorum	0%	0%	3.45%	0%	0%
Helicobacter pullorum	0%	0%	3.45%	0%	0%
Ruthenibacterium lactatiformans	0%	0%	3.33%	0%	0%
Ruthenibacterium lactatiformans	0%	0%	0%	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): 500

Protein
DNA

>gb|AAW34150.1|+|APH(2'')-If [Campylobacter jejuni]
MDIKKIIEEKCNIVVDSIKLIGEGYDSKAYIVNNEYVFKIKFSANKKKGYEKEKAIYDFLNKKLNTNIKIPNIEYSYISEELSILGYKEI
KGTFLTPEIYFALSKEKQELLKQDIAMFLRQMHDLDYSEISSYTIDNKQNVLEEYQLLKETIYDSLTDIEKQYVEEFMQRLNSTTIFDGK
KCLCHNDFSCNHLLLDDENRLCGVIDFGDSGIIDEYCDFIYLLEDSEEEIGVSFGEDILRLYGNIDISKAKEYQDVVEQYYPIETIVYGI
KNNRPDFIEKGRKEIYIRTRKDEKLRK

>gb|AY701528.1|+|9696-10589|APH(2'')-If [Campylobacter jejuni]
ATGGATATAAAAAAGATAATAGAAGAAAAATGCAATATAGTTGTTGATAGTATAAAGTTGATTGGTGAGGGTTATGACAGCAAAGCATAC
ATTGTAAATAATGAATATGTTTTCAAAATCAAATTTAGTGCTAATAAGAAAAAAGGGTATGAAAAAGAAAAAGCAATATATGATTTTCTA
AACAAAAAATTAAATACAAATATTAAAATACCAAATATAGAATATTCATATATAAGTGAAGAATTATCTATTTTAGGATATAAAGAAATT
AAAGGAACTTTTTTAACACCAGAAATATATTTTGCCTTATCAAAAGAAAAGCAAGAATTATTAAAGCAAGATATTGCTATGTTTTTAAGA
CAAATGCACGATTTAGATTATAGTGAAATAAGTTCATATACGATAGACAATAAACAAAATGTTTTAGAAGAATATCAATTACTTAAAGAA
ACAATATATGATAGTCTTACTGATATTGAAAAACAATATGTAGAAGAATTTATGCAAAGATTAAATAGTACAACTATATTTGATGGTAAA
AAATGCTTATGCCATAATGATTTTAGTTGTAATCATTTATTACTTGATGATGAAAATAGATTATGTGGTGTAATAGATTTTGGAGATTCT
GGAATTATAGATGAATACTGTGATTTCATATATTTGCTAGAAGATAGTGAAGAAGAAATTGGCGTGTCTTTTGGAGAAGATATATTAAGA
TTATACGGAAATATTGATATTTCAAAAGCAAAGGAATATCAAGATGTTGTAGAACAATATTATCCAATAGAAACTATTGTATATGGTATT
AAAAATAATAGACCTGATTTTATAGAAAAAGGTAGAAAAGAGATTTATATAAGAACTCGCAAAGATGAAAAATTAAGGAAGTGA

Curator Acknowledgements

Curator	Description	Most Recent Edit

APH(2'')-If

Prevalence: protein homolog model (view sequences)

Graph