How to identify antibiotic resistant genes in gene databases?

Question

[ramin.k2013]

I want to know how can I identify antibiotic resistant genes from the Gene Ontology (GO) databases.

Answer 1

[geneontologyhelp]

GO is intended to capture the natural function of genes, and although we have ontology terms that might help classify genes that function in the response to antibiotics, actual 'susceptibility/resistance' implies a phenotype rather than a biological process or molecular function (or our third aspect, cellular component) and is therefore outside the scope of GO.

If you would like to browse GO terms or find gene/gene products that have been annotated as a starting point, try the search options (see GO:0046677 response to antibiotic) or you can also find downloads linked from term pages like GO:0042742 defense response to bacterium. You can also use the GO API once you're more familiar with the GO. GO is commonly used for enrichment analysis, and the PANTHER EA on our homepage will accept UniProt IDs.

Answer 2

[patrickdm]

Not sure I understand your goal here, but The Comprehensive Antibiotic Resistance Database (CARD) should be a good reference resource. Hth

[ramin.k2013]

I already have a gene abundance table with uniref90 IDs, and I want to identify only the antibiotic resistant genes from the table and get rid of the others. I did not find any mapping reference from Uniref90 IDs (or UniportKB IDs) to CARD accession numbers to match them. Is there any ID mapping reference for CARD (mapping to any other databases)?

I have found a ID mapping reference from the uniport website, to other databases such as GO, but do not know how ARGs are distinguishable in GO.

[Mensur Dlakic]

Wow, how much a difference it makes when you explain the problem properly rather than a single-sentence explanation in your original post. But now it also makes it easier to realize that you have already asked the same question before.

By now you could have blasted your sequences of interest against CARD, as there is a good chance that ID translation doesn't exist for ARGs.

[ramin.k2013]

I think I have to do so. I could not find any mapping reference. Thank you.