Nucleic Acids Research, 2000, Vol. 28, No. 1 263-266
© 2000 Oxford University Press
The Pfam Protein Families Database
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, 1Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA and 2Center for Genomics Research, 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 WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at http://www.cgr.ki.se/Pfam/ and in the US at http://pfam.wustl.edu/ . The latest version (4.3) of Pfam contains 1815 families. These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package.
* To whom correspondence should be addressed. Tel: +44 1223 494950; Fax: +44 1223 494919; Email: agb@sanger.ac.uk
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A. L. Vettore, F. R. da Silva, E. L. Kemper, G. M. Souza, A. M. da Silva, M. I. T. Ferro, F. Henrique-Silva, E. A. Giglioti, M. V.F. Lemos, L. L. Coutinho, et al. Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane Genome Res., December 1, 2003; 13(12): 2725 - 2735. [Abstract] [Full Text] [PDF]
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B. Eisenhaber, M. Wildpaner, C. J. Schultz, G. H.H. Borner, P. Dupree, and F. Eisenhaber Glycosylphosphatidylinositol Lipid Anchoring of Plant Proteins. Sensitive Prediction from Sequence- and Genome-Wide Studies for Arabidopsis and Rice Plant Physiology, December 1, 2003; 133(4): 1691 - 1701. [Abstract] [Full Text]
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B. Borud, G. Mellgren, J. Lund, and M. Bakke Cloning and Characterization of a Novel Zinc Finger Protein that Modulates the Transcriptional Activity of Nuclear Receptors Mol. Endocrinol., November 1, 2003; 17(11): 2303 - 2319. [Abstract] [Full Text] [PDF]
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H. D. Thorell, K. Stenklo, J. Karlsson, and T. Nilsson A Gene Cluster for Chlorate Metabolism in Ideonella dechloratans Appl. Envir. Microbiol., September 1, 2003; 69(9): 5585 - 5592. [Abstract] [Full Text] [PDF]
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Y. Wei, T. W. Southworth, H. Kloster, M. Ito, A. A. Guffanti, A. Moir, and T. A. Krulwich Mutational Loss of a K+ and NH4+ Transporter Affects the Growth and Endospore Formation of Alkaliphilic Bacillus pseudofirmus OF4 J. Bacteriol., September 1, 2003; 185(17): 5133 - 5147. [Abstract] [Full Text] [PDF]
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L. Papazisi, T. S. Gorton, G. Kutish, P. F. Markham, G. F. Browning, D. K. Nguyen, S. Swartzell, A. Madan, G. Mahairas, and S. J. Geary The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain Rlow Microbiology, September 1, 2003; 149(9): 2307 - 2316. [Abstract] [Full Text] [PDF]
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N. Casals, P. Gomez-Puertas, J. Pie, C. Mir, R. Roca, B. Puisac, R. Aledo, J. Clotet, S. Menao, D. Serra, et al. Structural ({beta}{alpha})8 TIM Barrel Model of 3-Hydroxy-3-methylglutaryl-Coenzyme A Lyase J. Biol. Chem., August 1, 2003; 278(31): 29016 - 29023. [Abstract] [Full Text] [PDF]
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F. T.S. Nogueira, V. E. De Rosa Jr., M. Menossi, E. C. Ulian, and P. Arruda RNA Expression Profiles and Data Mining of Sugarcane Response to Low Temperature Plant Physiology, August 1, 2003; 132(4): 1811 - 1824. [Abstract] [Full Text] [PDF]
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A. Teplyakov, G. Obmolova, S. Y. Chu, J. Toedt, E. Eisenstein, A. J. Howard, and G. L. Gilliland Crystal Structure of the YchF Protein Reveals Binding Sites for GTP and Nucleic Acid J. Bacteriol., July 15, 2003; 185(14): 4031 - 4037. [Abstract] [Full Text] [PDF]
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J. McDermott and R. Samudrala Bioverse: functional, structural and contextual annotation of proteins and proteomes Nucleic Acids Res., July 1, 2003; 31(13): 3736 - 3737. [Abstract] [Full Text] [PDF]
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A. Koike, Y. Kobayashi, and T. Takagi Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource Genome Res., June 1, 2003; 13(6): 1231 - 1243. [Abstract] [Full Text] [PDF]
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K. Tajul-Arifin, R. Teasdale, T. Ravasi, D. A. Hume, RIKEN GER Group, GSL Members, and J. S. Mattick Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome Genome Res., June 1, 2003; 13(6): 1416 - 1429. [Abstract] [Full Text] [PDF]
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N. Lee, J. Chen, L. Sun, S. Wu, K. R. Gray, A. Rich, M. Huang, J.-H. Lin, J. N. Feder, E. B. Janovitz, et al. Expression and Characterization of Human Transient Receptor Potential Melastatin 3 (hTRPM3) J. Biol. Chem., May 30, 2003; 278(23): 20890 - 20897. [Abstract] [Full Text] [PDF]
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S. Chapuy-Regaud, A. D. Ogunniyi, N. Diallo, Y. Huet, J.-F. Desnottes, J. C. Paton, S. Escaich, and M.-C. Trombe RegR, a Global LacI/GalR Family Regulator, Modulates Virulence and Competence in Streptococcus pneumoniae Infect. Immun., May 1, 2003; 71(5): 2615 - 2625. [Abstract] [Full Text] [PDF]
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R. Seshadri, I. T. Paulsen, J. A. Eisen, T. D. Read, K. E. Nelson, W. C. Nelson, N. L. Ward, H. Tettelin, T. M. Davidsen, M. J. Beanan, et al. Complete genome sequence of the Q-fever pathogen Coxiellaburnetii PNAS, April 29, 2003; 100(9): 5455 - 5460. [Abstract] [Full Text] [PDF]
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P. F. Markham, A. Kanci, G. Czifra, B. Sundquist, P. Hains, and G. F. Browning Homologue of Macrophage-Activating Lipoprotein in Mycoplasmagallisepticum Is Not Essential for Growth and Pathogenicity in Tracheal Organ Cultures J. Bacteriol., April 15, 2003; 185(8): 2538 - 2547. [Abstract] [Full Text] [PDF]
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L. Li, E. I. Shakhnovich, and L. A. Mirny Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases PNAS, April 15, 2003; 100(8): 4463 - 4468. [Abstract] [Full Text] [PDF]
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C. Seoighe, C. R. Johnston, and D. C. Shields Significantly Different Patterns of Amino Acid Replacement After Gene Duplication as Compared to After Speciation Mol. Biol. Evol., April 1, 2003; 20(4): 484 - 490. [Abstract] [Full Text] [PDF]
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C. F. Brunk, L. C. Lee, A. B. Tran, and J. Li Complete sequence of the mitochondrial genome of Tetrahymena thermophila and comparative methods for identifying highly divergent genes Nucleic Acids Res., March 15, 2003; 31(6): 1673 - 1682. [Abstract] [Full Text] [PDF]
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D. Kerk, J. Bulgrien, D. W. Smith, and M. Gribskov Arabidopsis Proteins Containing Similarity to the Universal Stress Protein Domain of Bacteria Plant Physiology, March 1, 2003; 131(3): 1209 - 1219. [Abstract] [Full Text] [PDF]
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