Pfam Domain Annotation

Question

[Cotsapas]

Greetings all - we have annotated a set of proteins with pfam domain calls. We would like a higher-level view of domain space (eg, dna-binding, catalytic, protein-binding, etc) rather than specific families. Anyone know of a family annotation table somewhere?

Chris

Answer 1

[Khader Shameer]

You can use Pfam2GO annotations http://www.geneontology.org/external2go/pfam2go

This is an automated mapping of GO terms to Pfam domains. Please note that Pfam2GO annotations may not be available for all the domains.

[Michael Kuhn]

additionally, I would suggest using Pfam clans of domains to get likely GO annotations for terms that don't have them

[Khader Shameer]

Michael, I agree that Clans can provide a global view of related protein domain families in Pfam. IMHO deriving GO annotation from the CLAN members will be tricky at times. Clan level relation may not be the be the best pool to derive functions for families with out Pfam2GO.

[Cotsapas]

Thanks Khader - we'll try it and see. C

Answer 2

[User 6169]

If it's a small set of proteins, you can use ProtoNet: http://www.protonet.cs.huji.ac.il/ There is a tool "Classify Your Protein". ProtoNet provides automatic hierarchical classification of proteins according to sequences.