The Pfam Protein Families Database

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Dec 1

PMID 22127870

Citations 2114

Authors

Marco Punta

Penny C Coggill

Ruth Y Eberhardt

Jaina Mistry

John Tate

Chris Boursnell

Ningze Pang

Kristoffer Forslund

Goran Ceric

Jody Clements

Andreas Heger

Liisa Holm

Erik L L Sonnhammer

Sean R Eddy

Alex Bateman

Robert D Finn

Affiliations

Soon will be listed here.

Abstract

Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the 'sunburst' representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.

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References

Finn R, Mistry J, Tate J, Coggill P, Heger A, Pollington J . The Pfam protein families database. Nucleic Acids Res. 2009; 38(Database issue):D211-22. PMC: 2808889. DOI: 10.1093/nar/gkp985. View

Gomez T, Billadeau D . A FAM21-containing WASH complex regulates retromer-dependent sorting. Dev Cell. 2009; 17(5):699-711. PMC: 2803077. DOI: 10.1016/j.devcel.2009.09.009. View

Hunter S, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro: the integrative protein signature database. Nucleic Acids Res. 2008; 37(Database issue):D211-5. PMC: 2686546. DOI: 10.1093/nar/gkn785. View

Cantarel B, Coutinho P, Rancurel C, Bernard T, Lombard V, Henrissat B . The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2008; 37(Database issue):D233-8. PMC: 2686590. DOI: 10.1093/nar/gkn663. View

Sathiyamoorthy K, Mills E, Franzmann T, Rosenshine I, Saper M . The crystal structure of Escherichia coli group 4 capsule protein GfcC reveals a domain organization resembling that of Wza. Biochemistry. 2011; 50(24):5465-76. DOI: 10.1021/bi101869h. View

Kersey P, Lawson D, Birney E, Derwent P, Haimel M, Herrero J . Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res. 2009; 38(Database issue):D563-9. PMC: 2808935. DOI: 10.1093/nar/gkp871. View

Eddy S . A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol. 2008; 4(5):e1000069. PMC: 2396288. DOI: 10.1371/journal.pcbi.1000069. View

. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2009; 38(Database issue):D142-8. PMC: 2808944. DOI: 10.1093/nar/gkp846. View

Sigrist C, Cerutti L, de Castro E, Langendijk-Genevaux P, Bulliard V, Bairoch A . PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 2009; 38(Database issue):D161-6. PMC: 2808866. DOI: 10.1093/nar/gkp885. View

10.

Coggill P, Finn R, Bateman A . Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. 2008; Chapter 2:2.5.1-2.5.17. DOI: 10.1002/0471250953.bi0205s23. View

11.

Bateman A, Coggill P, Finn R . DUFs: families in search of function. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010; 66(Pt 10):1148-52. PMC: 2954198. DOI: 10.1107/S1744309110001685. View

12.

Murzin A, Brenner S, Hubbard T, Chothia C . SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995; 247(4):536-40. DOI: 10.1006/jmbi.1995.0159. View

13.

Jaroszewski L, Li Z, Sri Krishna S, Bakolitsa C, Wooley J, Deacon A . Exploration of uncharted regions of the protein universe. PLoS Biol. 2009; 7(9):e1000205. PMC: 2744874. DOI: 10.1371/journal.pbio.1000205. View

14.

Chen C, Natale D, Finn R, Huang H, Zhang J, Wu C . Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One. 2011; 6(4):e18910. PMC: 3083393. DOI: 10.1371/journal.pone.0018910. View

15.

Gardner P, Daub J, Tate J, Moore B, Osuch I, Griffiths-Jones S . Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res. 2010; 39(Database issue):D141-5. PMC: 3013711. DOI: 10.1093/nar/gkq1129. View

16.

Heger A, Holm L . Exhaustive enumeration of protein domain families. J Mol Biol. 2003; 328(3):749-67. DOI: 10.1016/s0022-2836(03)00269-9. View

17.

Suzek B, Huang H, McGarvey P, Mazumder R, Wu C . UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007; 23(10):1282-8. DOI: 10.1093/bioinformatics/btm098. View

18.

Zhao W, Fang G . Anillin is a substrate of anaphase-promoting complex/cyclosome (APC/C) that controls spatial contractility of myosin during late cytokinesis. J Biol Chem. 2005; 280(39):33516-24. DOI: 10.1074/jbc.M504657200. View

19.

Miyakawa T, Miyazono K, Sawano Y, Hatano K, Tanokura M . Crystal structure of ginkbilobin-2 with homology to the extracellular domain of plant cysteine-rich receptor-like kinases. Proteins. 2009; 77(1):247-51. DOI: 10.1002/prot.22494. View

20.

Hollich V, Sonnhammer E . PfamAlyzer: domain-centric homology search. Bioinformatics. 2007; 23(24):3382-3. DOI: 10.1093/bioinformatics/btm521. View