Pfam

Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.

Features
For each family in Pfam one can:

The descriptions of Pfam families are managed by the general public using Wikipedia.
 * Look at multiple alignments
 * View protein domain architectures
 * Examine species distribution
 * Follow links to other databases
 * View known protein structures

74% of protein sequences have at least one match to Pfam. This number is called the sequence coverage.

The Pfam database contains information about protein domains and families. Pfam-A is the manually curated portion of the database that contains over 10,000 entries. For each entry a protein sequence alignment and a hidden Markov model is stored. These hidden Markov models can be used to search sequence databases with the HMMER package written by Sean Eddy. Because the entries in Pfam-A do not cover all known proteins, an automatically generated supplement is provided called Pfam-B. Pfam-B contains a large number of small families derived from clusters produced by an algorithm called ADDA. Although of lower quality, Pfam-B families can be useful when no Pfam-A families are found.

The database iPfam builds on the domain description of Pfam. It investigates if different proteins described together in the protein structure database PDB are close enough to potentially interact.

The current release of Pfam is "Pfam 25.0" (March 2011; 12,273 families).