Pfam -- Protein Families Database

What you can do:
A comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models.
  • Pfam is a widely used database of protein families and domains.
  • There are two components to Pfam: Pfam-A and Pfam-B.
  • Pfam-A entries are high quality, manually curated families.
  • Although these Pfam-A entries cover a large proportion of the sequences in the underlying sequence database, in order to give a more comprehensive coverage of known proteins we also generate a supplement using the PRODOM database.
  • These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found.
  • Pfam also generates higher-level groupings of related families, known as clans.
  • A clan is a collection of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM.
  • The current released uses HMMER3, the latest version of the popular profile hidden Markov model package.
  • This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm.
  • Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years.
  • protein sequence alignments
  • multiple protein sequence alignment
  • protein structure alignments
  • homologous protein families
  • protein domains
  • protein domain architectures
Literature & Tutorials:
This record last updated: 02-01-2010
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