The Pfam protein families database

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


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, in Sweden at, in France at and in the US at 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.

MeSH terms

  • Animals
  • Binding Sites
  • Computer Graphics
  • Databases, Protein*
  • Evolution, Molecular
  • Genome
  • Humans
  • Information Storage and Retrieval
  • Internet
  • Macromolecular Substances
  • Markov Chains
  • Phylogeny
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / physiology
  • Sequence Alignment


  • Macromolecular Substances
  • Proteins