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Nucleic Acids Research 2006 34(Database Issue):D247-D251; doi:10.1093/nar/gkj149
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Nucleic Acids Research, 2006, Vol. 34, Database issue D247-D251
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Pfam: clans, web tools and services

Robert D. Finn*, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich1, Timo Lassmann1, Simon Moxon, Mhairi Marshall, Ajay Khanna2, Richard Durbin, Sean R. Eddy2, Erik L. L. Sonnhammer1 and Alex Bateman

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK 1Center for Genomics and Bioinformatics, Karolinska Institutet S-171 77 Stockholm, Sweden 2Department of Genetics, Howard Hughes Medical Institute, Washington University School of Medicine St Louis, MO 63110, USA

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

Received September 15, 2005. Revised October 19, 2005. Accepted October 28, 2005.

Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://pfam.cgb.ki.se/).


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 Nucleic Acids ResHome page
H. Y. K. Lam, E. Khurana, G. Fang, P. Cayting, N. Carriero, K.-H. Cheung, and M. B. Gerstein
Pseudofam: the pseudogene families database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D738 - D743.
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 Nucleic Acids ResHome page
V. G. Tarcea, T. Weymouth, A. Ade, A. Bookvich, J. Gao, V. Mahavisno, Z. Wright, A. Chapman, M. Jayapandian, A. Ozgur, et al.
Michigan molecular interactions r2: from interacting proteins to pathways
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D642 - D646.
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 Nucleic Acids ResHome page
R. A. Laskowski
PDBsum new things
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D355 - D359.
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D. Wilson, R. Pethica, Y. Zhou, C. Talbot, C. Vogel, M. Madera, C. Chothia, and J. Gough
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D380 - D386.
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 Nucleic Acids ResHome page
J. E. Mabey Gilsenan, G. Atherton, J. Bartholomew, P. F. Giles, T. K. Attwood, D. W. Denning, and P. Bowyer
Aspergillus Genomes and the Aspergillus Cloud
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D509 - D514.
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 BioinformaticsHome page
A. J. Bordner
Predicting small ligand binding sites in proteins using backbone structure
Bioinformatics, December 15, 2008; 24(24): 2865 - 2871.
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J.-P. Gagne, M. Isabelle, K. S. Lo, S. Bourassa, M. J. Hendzel, V. L. Dawson, T. M. Dawson, and G. G. Poirier
Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes
Nucleic Acids Res., December 1, 2008; 36(22): 6959 - 6976.
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M.-C. Shun, Y. Botbol, X. Li, F. Di Nunzio, J. E. Daigle, N. Yan, J. Lieberman, M. Lavigne, and A. Engelman
Identification and Characterization of PWWP Domain Residues Critical for LEDGF/p75 Chromatin Binding and Human Immunodeficiency Virus Type 1 Infectivity
J. Virol., December 1, 2008; 82(23): 11555 - 11567.
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 Mol Biol EvolHome page
D. Chalkia, N. Nikolaidis, W. Makalowski, J. Klein, and M. Nei
Origins and Evolution of the Formin Multigene Family That Is Involved in the Formation of Actin Filaments
Mol. Biol. Evol., December 1, 2008; 25(12): 2717 - 2733.
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 J. Biol. Chem.Home page
K. Fukui, N. Nakagawa, Y. Kitamura, Y. Nishida, R. Masui, and S. Kuramitsu
Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression
J. Biol. Chem., November 28, 2008; 283(48): 33417 - 33427.
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 Proc. Natl. Acad. Sci. USAHome page
A. J. Robinson, C. Overy, and E. R. S. Kunji
The mechanism of transport by mitochondrial carriers based on analysis of symmetry
PNAS, November 18, 2008; 105(46): 17766 - 17771.
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 J. Biol. Chem.Home page
Y. Zhang, J. Ju, H. Peng, F. Gao, C. Zhou, Y. Zeng, Y. Xue, Y. Li, B. Henrissat, G. F. Gao, et al.
Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A
J. Biol. Chem., November 14, 2008; 283(46): 31551 - 31558.
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 Proc. Natl. Acad. Sci. USAHome page
E. B. Rosenblum, J. E. Stajich, N. Maddox, and M. B. Eisen
Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis
PNAS, November 4, 2008; 105(44): 17034 - 17039.
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M. F. Del Papa and M. Perego
Ethanolamine Activates a Sensor Histidine Kinase Regulating Its Utilization in Enterococcus faecalis
J. Bacteriol., November 1, 2008; 190(21): 7147 - 7156.
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 The Plant GenomeHome page
M. W. Vasconcelos, G. W. Li, M. A. Lubkowitz, and M. A. Grusak
Characterization of the PT Clade of Oligopeptide Transporters in Rice
The Plant Genome, November 1, 2008; 1(2): 77 - 88.
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 BioinformaticsHome page
R. F. de Souza, V. Anantharaman, S. J. de Souza, L. Aravind, and F. J. Gueiros-Filho
AMIN domains have a predicted role in localization of diverse periplasmic protein complexes
Bioinformatics, November 1, 2008; 24(21): 2423 - 2426.
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 BioinformaticsHome page
F. Jadeau, E. Bechet, A. J. Cozzone, G. Deleage, C. Grangeasse, and C. Combet
Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature
Bioinformatics, November 1, 2008; 24(21): 2427 - 2430.
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 Mol Biol EvolHome page
K. Somogyi, B. Sipos, Z. Penzes, E. Kurucz, J. Zsamboki, D. Hultmark, and I. Ando
Evolution of Genes and Repeats in the Nimrod Superfamily
Mol. Biol. Evol., November 1, 2008; 25(11): 2337 - 2347.
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 Plant Physiol.Home page
A. S. Rajangam, M. Kumar, H. Aspeborg, G. Guerriero, L. Arvestad, P. Pansri, C. J.-L. Brown, S. Hober, K. Blomqvist, C. Divne, et al.
MAP20, a Microtubule-Associated Protein in the Secondary Cell Walls of Hybrid Aspen, Is a Target of the Cellulose Synthesis Inhibitor 2,6-Dichlorobenzonitrile
Plant Physiology, November 1, 2008; 148(3): 1283 - 1294.
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