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Database that has all known proteins associated with a particular PFAM or TIGRFAM?

Are there any databases or tools that have every protein that is associated with a particular PFAM or TIGRFAM?

I'm assuming that there will be more for PFAM since they have been around for quite some time but it would be really useful if there was a tool I could use. Online GUI would be good and a Python package would be good as well.

pfam tigrfam protein database gene
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updated by Ram Ram • written by jolespin jolespin

2 answers

UniProt sounds like the solution you are looking for. The examples below works for both pfam and TIGRFAM, and you can use logic. E.g., PF02171 OR TIGR00008.

Web results: http://www.uniprot.org/uniprot/?query=PF02171&sort=score

Downloadable/programmatic: http://www.uniprot.org/uniprot/?query=PF02171&format=tab

Details on how to use to API: http://www.uniprot.org/help/programmatic_access

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updated by Ram Ram • written by David Westergaard David Westergaard

Hi jolespin,

Would this resource be of help to you - http://www.geneontology.org/external2go/pfam2go?

It seems you just need a quick script to extract the list of PFAM domains you are interested in. Also, if this does not provide all relevant detail, as noted in the header, the citation is

!citation: Mitchell et al. (2015) Nucl. Acids Res. 43 :D213-D221

So reading there might let you know what other resources are available.

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updated by Ram Ram • written by LauferVA LauferVA

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