Pfam -- Protein Families Database

URL:

http://pfam.janelia.org/

What you can do:

A comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models.

Highlights:

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.

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This record last updated: 02-01-2010