Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. For each family in Pfam you can:
1. Look at multiple alignments
2. View protein domain architectures
3. Examine species distribution
4. Follow links to other databases
5. View known protein structures
For more information on Pfam, on using this site, or on the changes between Pfam releases 7 and 8, visit www.sanger.ac.uk/Software/Pfam/help/index.shtml
Pfam can be used to view the domain organisation of proteins. A typical example is shown below. Notice that a single protein can belong to several Pfam families.
73% of protein sequences have at least one match to Pfam. This number is called the sequence coverage.
Pfam is a database of two parts, the first is the curated part of Pfam containing over 5193 protein families. To give Pfam a more comprehensive coverage of known proteins we automatically generate a supplement called Pfam-B. This contains a large number of small families taken from the PRODOM database that do not overlap with Pfam-A. Although of lower quality Pfam-B families can be useful when no Pfam-A families are found.