doi: 10.1093/nar/gkm960. Epub 2007 Nov 26.
The Pfam protein families database
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- PMID:18039703
- PMCID: PMC2238907
- DOI: 10.1093/nar/gkm960
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The Pfam protein families database
Robert D Finn et al. Nucleic Acids Res.2008 Jan.
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Abstract
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metagenomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/).
Figures
The Pfam family page from the new website. This page shows the summary information for the Piwi domain. The tabs on the left allow users to browse the different types of associated information and beneath the tabs is the ‘jump to’ box, a tool which can direct the user to the page for any other entry in the site, given any type of accession or identifier. The panel at the top right gives a summary of the number of protein architectures, sequences, interactions, species and structures available. The same page layout and navigational tools are common to all of the different types of data in the Pfam website.
The Pfam protein sequence page, showing the DAS annotation viewer. Various tracks can be selected using the check boxes beneath the annotation view, allowing the user to view features derived from any of the listed DAS sources. For instance, in the example displayed, the membrane topology calculated by Phobius (18) can be viewed alongside the Pfam domain annotations and those from a variety of different domain databases. The figure shows a tool-tip for one feature, which gives the details of the annotation and, in this case, highlights the link to further information.
The DAS-based Pfam sequence alignment viewer. A portion of the Piwi domain full alignment is shown with residue conservation highlighted in a ClustalX (19) style colour scheme.
References
- Sonnhammer ELL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997;28:405–420. - PubMed
- Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, et al. The Universal Protein Resource (UniProt) Nucleic Acids Res. 2007;35:D193–D197.
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