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Nucleic Acids Research Advance Access published online on November 26, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm960
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The Pfam protein families database

Robert D. Finn1,*, John Tate1, Jaina Mistry1, Penny C. Coggill1, Stephen John Sammut1, Hans-Rudolf Hotz1, Goran Ceric2, Kristoffer Forslund3, Sean R. Eddy2, Erik L. L. Sonnhammer3 and Alex Bateman1

1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK, 2Howard Hughes Medical Institute Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA and 3Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden

*To whom correspondence should be addressed. Tel: +44 1223 495330; Fax: +44 1223 494919; Email: rdf{at}sanger.ac.uk

Received September 15, 2007. Revised October 10, 2007. Accepted October 16, 2007.

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/).


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The C-Ala Domain Brings Together Editing and Aminoacylation Functions on One tRNA
Science, August 7, 2009; 325(5941): 744 - 747.
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 J. Biol. Chem.Home page
Q. H. Christensen and J. E. Cronan
The Thermoplasma acidophilum LplA-LplB Complex Defines a New Class of Bipartite Lipoate-protein Ligases
J. Biol. Chem., August 7, 2009; 284(32): 21317 - 21326.
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 DatabaseHome page
L. Wissler, E. Dattolo, A. D. Moore, T. B. H. Reusch, J. L. Olsen, M. Migliaccio, E. Bornberg-Bauer, and G. Procaccini
Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs
Database, August 4, 2009; 2009(0): bap009 - bap009.
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 J. Bacteriol.Home page
A. Piotrowski, P. Burghout, and D. A. Morrison
spr1630 Is Responsible for the Lethality of clpX Mutations in Streptococcus pneumoniae
J. Bacteriol., August 1, 2009; 191(15): 4888 - 4895.
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 Nucleic Acids ResHome page
S. A. McMahon, G. A. Roberts, K. A. Johnson, L. P. Cooper, H. Liu, J. H. White, L. G. Carter, B. Sanghvi, M. Oke, M. D. Walkinshaw, et al.
Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance
Nucleic Acids Res., August 1, 2009; 37(15): 4887 - 4897.
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 BioinformaticsHome page
A. F. Neuwald
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
Bioinformatics, August 1, 2009; 25(15): 1869 - 1875.
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 Biol. Reprod.Home page
J. Tejomurtula, K.-B. Lee, S. K. Tripurani, G. W. Smith, and J. Yao
Role of Importin Alpha8, a New Member of the Importin Alpha Family of Nuclear Transport Proteins, in Early Embryonic Development in Cattle
Biol Reprod, August 1, 2009; 81(2): 333 - 342.
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 J. Bacteriol.Home page
J. C. Setubal, P. dos Santos, B. S. Goldman, H. Ertesvag, G. Espin, L. M. Rubio, S. Valla, N. F. Almeida, D. Balasubramanian, L. Cromes, et al.
Genome Sequence of Azotobacter vinelandii, an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes
J. Bacteriol., July 15, 2009; 191(14): 4534 - 4545.
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 J. Biol. Chem.Home page
Y.-J. Pan, C.-C. Cho, Y.-Y. Kao, and C.-H. Sun
A Novel WRKY-like Protein Involved in Transcriptional Activation of Cyst Wall Protein Genes in Giardia lamblia
J. Biol. Chem., July 3, 2009; 284(27): 17975 - 17988.
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 MicrobiologyHome page
S. Kimura, Y. Shiraiwa, and I. Suzuki
Function of the N-terminal region of the phosphate-sensing histidine kinase, SphS, in Synechocystis sp. PCC 6803
Microbiology, July 1, 2009; 155(7): 2256 - 2264.
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 Nucleic Acids ResHome page
B. W. Brandt and J. Heringa
webPRC: the Profile Comparer for alignment-based searching of public domain databases
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W48 - W52.
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 Nucleic Acids ResHome page
R. I. Sadreyev, M. Tang, B.-H. Kim, and N. V. Grishin
COMPASS server for homology detection: improved statistical accuracy, speed and functionality
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W90 - W94.
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 Nucleic Acids ResHome page
C.-C. Chen, C.-Y. Lin, Y.-S. Lo, and J.-M. Yang
PPISearch: a web server for searching homologous protein-protein interactions across multiple species
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W369 - W375.
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 Nucleic Acids ResHome page
J. Bruggeman, J. Heringa, and B. W. Brandt
PhyloPars: estimation of missing parameter values using phylogeny
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W179 - W184.
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 Nucleic Acids ResHome page
A. Rose, S. Lorenzen, A. Goede, B. Gruening, and P. W. Hildebrand
RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W575 - W580.
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 Nucleic Acids ResHome page
S. Shridhar, D. Chattopadhyay, and G. Yadav
PLecDom: a program for identification and analysis of plant lectin domains
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W452 - W458.
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 Nucleic Acids ResHome page
D. T.-H. Chang, T.-Y. Chien, and C.-Y. Chen
seeMotif: exploring and visualizing sequence motifs in 3D structures
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W552 - W558.
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 Nucleic Acids ResHome page
A. Kuzniar, K. Lin, Y. He, H. Nijveen, S. Pongor, and J. A. M. Leunissen
ProGMap: an integrated annotation resource for protein orthology
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W428 - W434.
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 Nucleic Acids ResHome page
H. Blankenburg, F. Ramirez, J. Buch, and M. Albrecht
DASMIweb: online integration, analysis and assessment of distributed protein interaction data
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W122 - W128.
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 J. Biol. Chem.Home page
M. Sandoval-Calderon, O. Geiger, Z. Guan, F. Barona-Gomez, and C. Sohlenkamp
A Eukaryote-like Cardiolipin Synthase Is Present in Streptomyces coelicolor and in Most Actinobacteria
J. Biol. Chem., June 26, 2009; 284(26): 17383 - 17390.
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S. Ehira, H. Ogino, H. Teramoto, M. Inui, and H. Yukawa
Regulation of Quinone Oxidoreductase by the Redox-sensing Transcriptional Regulator QorR in Corynebacterium glutamicum
J. Biol. Chem., June 19, 2009; 284(25): 16736 - 16742.
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 BioinformaticsHome page
O. Fornes, R. Aragues, J. Espadaler, M. A. Marti-Renom, A. Sali, and B. Oliva
ModLink+: improving fold recognition by using protein-protein interactions
Bioinformatics, June 15, 2009; 25(12): 1506 - 1512.
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 BioinformaticsHome page
J. Ramana and D. Gupta
ProtVirDB: a database of protozoan virulent proteins
Bioinformatics, June 15, 2009; 25(12): 1568 - 1569.
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 BioinformaticsHome page
X. Guo and A. J. Hartemink
Domain-oriented edge-based alignment of protein interaction networks
Bioinformatics, June 15, 2009; 25(12): i240 - 1246.
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