Nucleic Acids Research, 2002, Vol. 30, No. 1 276-280
© 2002 Oxford University Press
The Pfam Protein Families Database
Wellcome Trust Sanger Institute and 1The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, 2SIB, ISREC, 155, ch. des Boveresses, CH-1066 Epalinges s/Lausanne, Switzerland, 3Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA and 4Center for Genomics and Bioinformatics, Karolinska Institutet, S-171 77 Stockholm, Sweden
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
* To whom correspondence should be addressed. Tel: +44 1223 494950; Fax: +44 1223 494919; Email: agb{at}sanger.ac.uk
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L. Feng, A. V. Perepelov, G. Zhao, S. D. Shevelev, Q. Wang, S. N. Senchenkova, A. S. Shashkov, Y. Geng, P. R. Reeves, Y. A. Knirel, et al. Structural and genetic evidence that the Escherichia coli O148 O antigen is the precursor of the Shigella dysenteriae type 1 O antigen and identification of a glucosyltransferase gene Microbiology, January 1, 2007; 153(1): 139 - 147. [Abstract] [Full Text] [PDF]
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M. Tian, J. Win, J. Song, R. van der Hoorn, E. van der Knaap, and S. Kamoun A Phytophthora infestans Cystatin-Like Protein Targets a Novel Tomato Papain-Like Apoplastic Protease Plant Physiology, January 1, 2007; 143(1): 364 - 377. [Abstract] [Full Text] [PDF]
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R. A. Rampey, A. W. Woodward, B. N. Hobbs, M. P. Tierney, B. Lahner, D. E. Salt, and B. Bartel An Arabidopsis Basic Helix-Loop-Helix Leucine Zipper Protein Modulates Metal Homeostasis and Auxin Conjugate Responsiveness Genetics, December 1, 2006; 174(4): 1841 - 1857. [Abstract] [Full Text] [PDF]
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M. G. Muszynski, T. Dam, B. Li, D. M. Shirbroun, Z. Hou, E. Bruggemann, R. Archibald, E. V. Ananiev, and O. N. Danilevskaya delayed flowering1 Encodes a Basic Leucine Zipper Protein That Mediates Floral Inductive Signals at the Shoot Apex in Maize Plant Physiology, December 1, 2006; 142(4): 1523 - 1536. [Abstract] [Full Text] [PDF]
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S. S. Mendiratta, N. Sekulic, F. G. Hernandez-Guzman, B. E. Close, A. Lavie, and K. J. Colley A Novel {alpha}-Helix in the First Fibronectin Type III Repeat of the Neural Cell Adhesion Molecule Is Critical for N-Glycan Polysialylation J. Biol. Chem., November 24, 2006; 281(47): 36052 - 36059. [Abstract] [Full Text] [PDF]
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N. Przulj and D. J Higham Modelling protein-protein interaction networks via a stickiness index J R Soc Interface, October 22, 2006; 3(10): 711 - 716. [Abstract] [Full Text] [PDF]
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P. Marttinen, J. Corander, P. Toronen, and L. Holm Bayesian search of functionally divergent protein subgroups and their function specific residues Bioinformatics, October 15, 2006; 22(20): 2466 - 2474. [Abstract] [Full Text] [PDF]
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W. G. Reeve, L. Brau, J. Castelli, G. Garau, C. Sohlenkamp, O. Geiger, M. J. Dilworth, A. R. Glenn, J. G. Howieson, and R. P. Tiwari The Sinorhizobium medicae WSM419 lpiA gene is transcriptionally activated by FsrR and required to enhance survival in lethal acid conditions. Microbiology, October 1, 2006; 152(Pt 10): 3049 - 3059. [Abstract] [Full Text] [PDF]
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K. Lin, L. Zhu, and D.-Y. Zhang An initial strategy for comparing proteins at the domain architecture level Bioinformatics, September 1, 2006; 22(17): 2081 - 2086. [Abstract] [Full Text] [PDF]
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S. R. Bushell, S. P. Bottomley, J. Rossjohn, and T. Beddoe Tracking the Unfolding Pathway of a Multirepeat Protein via Tryptophan Scanning: EVIDENCE OF LOCALIZED INSTABILITY IN THE MITOCHONDRIAL IMPORT RECEPTOR Tom70 J. Biol. Chem., August 25, 2006; 281(34): 24345 - 24350. [Abstract] [Full Text] [PDF]
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