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.

Nearly 80% of protein sequences in the UniProt Knowledgebase 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 16,000 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. Pfam-B was discontinued as of release 28.0.