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The Pfam Protein Families Database
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Abstract
Pfam is a large collection of protein multiple sequence alignments and profile hidden
Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/,
in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and
in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071
families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data,
where available, have been utilised to ensure that Pfam families correspond with structural
domains, and to improve domain-based annotation. Predictions of non-domain regions
are now also included. In addition to secondary structure, Pfam multiple sequence
alignments now contain active site residue mark-up. New search tools, including taxonomy
search and domain query, greatly add to the functionality and usability of the Pfam
resource.