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. 2002 Jan 1;30(1):276-80.
doi: 10.1093/nar/30.1.276.

The Pfam protein families database

Alex Bateman  1 , Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R Eddy, Sam Griffiths-Jones, Kevin L Howe, Mhairi Marshall, Erik L L Sonnhammer
Affiliations

The Pfam protein families database

Alex Bateman et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
The web view of the structural complex of thrombin with bovine pancreatic trypsin inhibitor. The web page shows the Pfam domain structure of the two proteins in the complex; the regions of the proteins represented in the PDB structure are highlighted by the square bracket above each protein. The protein structure picture has been kindly provided by the PDBsum resource (17).
Figure 2
Figure 2
Distribution of active site residues in SWISS-PROT and Pfam seed alignments. Histogram showing the frequency of amino acids found in active sites from SWISS-PROT (blue) and the frequency of amino acids aligned to active site residues (yellow).
See this image and copyright information in PMC

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