linG

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Accession	ARO:3002879
CARD Short Name	linG
Definition	linG is an integron-associated gene cassette, with aadA2, encoding a lincosomide nucleotidyltransferase found in Salmonella enterica. linG confers resistance to lincosomide antibiotics.
AMR Gene Family	lincosamide nucleotidyltransferase (LNU)
Drug Class	lincosamide antibiotic
Resistance Mechanism	antibiotic inactivation
Resistomes with Perfect Matches	Citrobacter freundii^wgs, Enterobacter asburiae^wgs, Enterobacter cloacae^p+wgs, Enterobacter hormaechei^p+wgs, Enterobacter roggenkampii^p, Escherichia albertii^p+wgs, Escherichia coli^g+p+wgs, Escherichia fergusonii^wgs, Klebsiella pneumoniae^p+wgs, Klebsiella quasipneumoniae^wgs, Proteus mirabilis^g+wgs+gi, Proteus penneri^wgs, Proteus vulgaris^p, Providencia rettgeri^wgs, Salmonella enterica^g+p+wgs, Shigella flexneri^p, Shigella sonnei^wgs
Resistomes with Sequence Variants	Citrobacter freundii^wgs, Enterobacter asburiae^wgs, Enterobacter cloacae^p+wgs, Enterobacter hormaechei^p+wgs, Enterobacter roggenkampii^p, Escherichia albertii^p+wgs, Escherichia coli^g+p+wgs, Escherichia fergusonii^g+p+wgs, Klebsiella oxytoca^p, Klebsiella pneumoniae^p+wgs, Klebsiella quasipneumoniae^wgs, Proteus mirabilis^g+wgs+gi, Proteus penneri^wgs, Proteus vulgaris^p, Providencia rettgeri^g+p+wgs, Salmonella enterica^g+p+wgs, Shigella boydii^wgs, Shigella flexneri^p, Shigella sonnei^wgs
Classification	8 ontology terms \| Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + determinant of antibiotic resistance + antibiotic molecule + antibiotic inactivation [Resistance Mechanism] + antibiotic inactivation enzyme + nucleotidylation of antibiotic conferring resistance + lincosamide antibiotic [Drug Class]
Parent Term(s)	2 ontology terms \| Show + confers_resistance_to_antibiotic lincomycin [Antibiotic] + lincosamide nucleotidyltransferase (LNU) [AMR Gene Family]
Publications	Levings RS, et al. 2006. Antimicrob Agents Chemother 50(10): 3514-3515. linG, a new integron-associated gene cassette encoding a lincosamide nucleotidyltransferase. (PMID 17005845)

Resistomes

Prevalence of linG 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)

Species	NCBI Chromosome	NCBI Plasmid	NCBI WGS	NCBI GI
Citrobacter freundii	0%	0%	0.19%	0%
Citrobacter freundii	0%	0%	0.39%	0%
Enterobacter asburiae	0%	0%	0.4%	0%
Enterobacter asburiae	0%	0%	0.4%	0%
Enterobacter cloacae	0%	0.56%	0.96%	0%
Enterobacter cloacae	0%	0.56%	0.64%	0%
Enterobacter hormaechei	0%	0.06%	0.22%	0%
Enterobacter hormaechei	0%	0.06%	0.13%	0%
Enterobacter roggenkampii	0%	0.48%	0%	0%
Enterobacter roggenkampii	0%	0.48%	0%	0%
Escherichia albertii	0%	0.56%	0.65%	0%
Escherichia albertii	0%	0.56%	0.65%	0%
Escherichia coli	0.02%	0.27%	0.7%	0%
Escherichia coli	0.05%	0.47%	1.19%	0%
Escherichia fergusonii	0%	0%	4.35%	0%
Escherichia fergusonii	1.64%	0.71%	9.78%	0%
Klebsiella oxytoca	0%	0.68%	0%	0%
Klebsiella oxytoca	0%	0%	0%	0%
Klebsiella pneumoniae	0%	0.01%	0.07%	0%
Klebsiella pneumoniae	0%	0.02%	0.17%	0%
Klebsiella quasipneumoniae	0%	0%	0.13%	0%
Klebsiella quasipneumoniae	0%	0%	0.53%	0%
Proteus mirabilis	2.75%	0%	2.81%	3.7%
Proteus mirabilis	2.75%	0%	1.82%	3.7%
Proteus penneri	0%	0%	12.5%	0%
Proteus penneri	0%	0%	12.5%	0%
Proteus vulgaris	0%	11.11%	0%	0%
Proteus vulgaris	0%	11.11%	0%	0%
Providencia rettgeri	0%	0%	0.64%	0%
Providencia rettgeri	2.94%	2.7%	5.1%	0%
Salmonella enterica	0.88%	1.97%	1.04%	0%
Salmonella enterica	0.88%	1.81%	0.98%	0%
Shigella boydii	0%	0%	0%	0%
Shigella boydii	0%	0%	1.11%	0%
Shigella flexneri	0%	1.2%	0%	0%
Shigella flexneri	0%	0.8%	0%	0%
Shigella sonnei	0%	0%	0.44%	0%
Shigella sonnei	0%	0%	0.15%	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|ABG65740.1|+|linG [Salmonella enterica subsp. enterica serovar Stanley]
MLQLKMIELFKEGCHEDARIIAALMFGSFAIGEGDEFSDIEFAVFIQDDHFENFDQRSWLNAVSPVAAYFPDDFGHHTALFENGIRGEFH
FMRKSDIPVISTWQGYGWFPSLEAAVLLDRSGELSRYASALVGGPPIREGAPLVEGLVLNLISLMLFGANLLNRGEYARAWALLSKAHEN
LLKLVRLHEGATDHWPTPSRALEKDISEDSYNRYLACTSSAEPRALCAAYHQTWTWSLELFKSVTEPLNIELPRTVIAQAKRLLNESATP
HNK

>gb|DQ836009.1|+|1310-2131|linG [Salmonella enterica subsp. enterica serovar Stanley]
ATGCTTCAGCTGAAAATGATCGAACTCTTCAAGGAAGGTTGTCATGAGGATGCACGAATAATCGCGGCATTGATGTTCGGCTCATTTGCT
ATCGGAGAGGGTGACGAGTTCTCTGATATCGAATTCGCAGTGTTCATCCAGGATGACCATTTTGAAAATTTCGATCAGCGCTCGTGGCTT
AATGCCGTAAGTCCGGTTGCTGCTTACTTTCCGGACGACTTCGGCCACCACACCGCACTTTTTGAAAACGGCATTCGCGGTGAATTCCAT
TTCATGCGAAAATCGGACATACCGGTCATTTCCACTTGGCAAGGCTATGGGTGGTTTCCCTCGCTTGAGGCGGCTGTTTTGTTGGACCGA
TCAGGAGAGTTGTCAAGGTACGCAAGCGCTCTCGTGGGCGGTCCCCCGATACGTGAAGGCGCGCCGCTGGTGGAAGGGCTTGTGTTGAAC
CTCATCAGCCTGATGCTCTTTGGGGCCAATCTTTTAAATCGGGGAGAGTACGCTCGCGCCTGGGCTTTGCTCAGCAAAGCACATGAAAAC
CTACTCAAGCTGGTTCGACTCCACGAAGGGGCAACAGACCACTGGCCGACACCTTCACGCGCGCTCGAAAAGGATATCTCGGAGGACTCG
TATAATCGCTATCTGGCATGCACAAGCAGTGCAGAACCAAGAGCACTATGTGCAGCCTATCATCAAACGTGGACGTGGAGTCTCGAATTG
TTCAAGAGCGTGACAGAACCTCTGAATATCGAGCTTCCGAGAACTGTAATTGCGCAGGCAAAAAGGTTGCTCAATGAGTCTGCGACGCCG
CACAACAAGTAA

linG

Prevalence: protein homolog model (view sequences)

Graph