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. 2000 Jan 1;28(1):263-6.
doi: 10.1093/nar/28.1.263.

The Pfam protein families database

A Bateman  1 , E Birney, R Durbin, S R Eddy, K L Howe, E L Sonnhammer
Affiliations

The Pfam protein families database

A Bateman et al. Nucleic Acids Res. .

Abstract

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgr.ki.se/Pfam/ and in the US at http://pfam.wustl.edu/. The latest version (4.3) of Pfam contains 1815 families. These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package.

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Figures

Figure 1
Figure 1
NIFAS view of the Pfam family Pep-utilizers (PF00391). Only members in the seed alignment are shown. Each sequence in the tree is shown with name/organism and Pfam domains as coloured boxes. Large boxes are Pfam-A domains while thin multi-coloured boxes are Pfam-B domains. The domains that were used to calculate the tree are marked with a small tree icon (green domains). The tree was calculated by Clustalw with bootstrapping. If a node has >90% bootstrap support it is marked with a green box; 75–90% with a yellow box; 50–75% with a white box; and 0–50% with no box.
Figure 2
Figure 2
Two possible types of overlap between Pfam-A and ProDom families are shown. (a) A partial overlap that gives one Pfam-B family. (b) A case where the Pfam-A family is subsumed by a ProDom family to create three numbered Pfam-B families.
See this image and copyright information in PMC

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