Nucleic Acids Research, Vol 27, Issue 1 260-262, Copyright © 1999 by Oxford University Press
A Bateman, E Birney, R Durbin, SR Eddy, RD Finn and EL Sonnhammer
Pfam is a collection of multiple alignments and profile hidden Markov
models of protein domain families. Release 3.1 is a major update of the
Pfam database and contains 1313 families which are available on the World
Wide Web in Europe at http://www.sanger.ac.uk/Software/Pfam/ and
http://www.cgr.ki.se/Pfam/, and in the US at http://pfam.wustl.edu/. Over
54% of proteins in SWISS-PROT-35 and SP-TrEMBL-5 match a Pfam family. The
primary changes of Pfam since release 2.1 are that we now use the more
advanced version 2 of the HMMER software, which is more sensitive and
provides expectation values for matches, and that it now includes proteins
from both SP-TrEMBL and SWISS-PROT.
ARTICLES
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. agb@sanger.ac.uk
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N. Mitsuhashi, T. Miki, H. Senbongi, N. Yokoi, H. Yano, M. Miyazaki, N. Nakajima, T. Iwanaga, Y. Yokoyama, T. Shibata, et al. MTABC3, a Novel Mitochondrial ATP-binding Cassette Protein Involved in Iron Homeostasis J. Biol. Chem., June 2, 2000; 275(23): 17536 - 17540. [Abstract] [Full Text] [PDF]
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A.-M. Mallon, M. Platzer, R. Bate, G. Gloeckner, M.R.M. Botcherby, G. Nordsiek, M.A. Strivens, P. Kioschis, A. Dangel, D. Cunningham, et al. Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man Genome Res., June 1, 2000; 10(6): 758 - 775. [Abstract] [Full Text]
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C.J. J. Francoijs, J. P.G. Klomp, and R. M.A. Knegtel Sequence annotation of nuclear receptor ligand-binding domains by automated homology modeling Protein Eng. Des. Sel., June 1, 2000; 13(6): 391 - 394. [Abstract] [Full Text] [PDF]
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J. G. Henikoff and S. Henikoff Drosophila Genomic Sequence Annotation Using the BLOCKS+ Database Genome Res., April 1, 2000; 10(4): 543 - 546. [Abstract] [Full Text]
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M. T. Bedford, D. Sarbassova, J. Xu, P. Leder, and M. B. Yaffe A Novel Pro-Arg Motif Recognized by WW Domains J. Biol. Chem., March 31, 2000; 275(14): 10359 - 10369. [Abstract] [Full Text] [PDF]
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G. M. Rubin, M. D. Yandell, J. R. Wortman, G. L. Gabor Miklos, C. R. Nelson, I. K. Hariharan, M. E. Fortini, P. W. Li, R. Apweiler, W. Fleischmann, et al. Comparative Genomics of the Eukaryotes Science, March 24, 2000; 287(5461): 2204 - 2215. [Abstract] [Full Text]
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J.E. Bray, A.E. Todd, F.M.G. Pearl, J.M. Thornton, and C.A. Orengo The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues Protein Eng. Des. Sel., March 1, 2000; 13(3): 153 - 165. [Abstract] [Full Text] [PDF]
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S. Güler, B. Essigmann, and C. Benning A Cyanobacterial Gene, sqdX, Required for Biosynthesis of the Sulfolipid Sulfoquinovosyldiacylglycerol J. Bacteriol., January 15, 2000; 182(2): 543 - 545. [Abstract] [Full Text]
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G. Yona, N. Linial, and M. Linial ProtoMap: automatic classification of protein sequences and hierarchy of protein families Nucleic Acids Res., January 1, 2000; 28(1): 49 - 55. [Abstract] [Full Text] [PDF]
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N. J. Schisler and J. D. Palmer The IDB and IEDB: intron sequence and evolution databases Nucleic Acids Res., January 1, 2000; 28(1): 181 - 184. [Abstract] [Full Text] [PDF]
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T. K. Attwood, M. D. R. Croning, D. R. Flower, A. P. Lewis, J. E. Mabey, P. Scordis, J. N. Selley, and W. Wright PRINTS-S: the database formerly known as PRINTS Nucleic Acids Res., January 1, 2000; 28(1): 225 - 227. [Abstract] [Full Text] [PDF]
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J. G. Henikoff, E. A. Greene, S. Pietrokovski, and S. Henikoff Increased coverage of protein families with the Blocks Database servers Nucleic Acids Res., January 1, 2000; 28(1): 228 - 230. [Abstract] [Full Text] [PDF]
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J. Murvai, K. Vlahovicek, E. Barta, B. Cataletto, and S. Pongor The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments Nucleic Acids Res., January 1, 2000; 28(1): 260 - 262. [Abstract] [Full Text] [PDF]
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A. Bateman, E. Birney, R. Durbin, S. R. Eddy, K. L. Howe, and E. L. L. Sonnhammer The Pfam Protein Families Database Nucleic Acids Res., January 1, 2000; 28(1): 263 - 266. [Abstract] [Full Text] [PDF]
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F. Corpet, F. Servant, J. Gouzy, and D. Kahn ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons Nucleic Acids Res., January 1, 2000; 28(1): 267 - 269. [Abstract] [Full Text] [PDF]
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A. Krause, J. Stoye, and M. Vingron The SYSTERS protein sequence cluster set Nucleic Acids Res., January 1, 2000; 28(1): 270 - 272. [Abstract] [Full Text] [PDF]
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H. Huang, C. Xiao, and C. H. Wu ProClass protein family database Nucleic Acids Res., January 1, 2000; 28(1): 273 - 276. [Abstract] [Full Text] [PDF]
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R. Kikuno, T. Nagase, M. Suyama, M. Waki, M. Hirosawa, and O. Ohara HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project Nucleic Acids Res., January 1, 2000; 28(1): 331 - 332. [Abstract] [Full Text] [PDF]
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M. D'Souza, M. F. Romine, and N. Maltsev SENTRA, a database of signal transduction proteins Nucleic Acids Res., January 1, 2000; 28(1): 335 - 336. [Abstract] [Full Text] [PDF]
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P. D. Rabinowicz, E. L. Braun, A. D. Wolfe, B. Bowen, and E. Grotewold Maize R2R3 Myb Genes: Sequence Analysis Reveals Amplification in the Higher Plants Genetics, September 1, 1999; 153(1): 427 - 444. [Abstract] [Full Text]
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H Stenmark and R Aasland FYVE-finger proteins--effectors of an inositol lipid J. Cell Sci., January 12, 1999; 112(23): 4175 - 4183. [Abstract] [PDF]
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S. Zimmer, A. Stocker, M. N. Sarbolouki, S. E. Spycher, J. Sassoon, and A. Azzi A Novel Human Tocopherol-associated Protein. CLONING, IN VITRO EXPRESSION, AND CHARACTERIZATION J. Biol. Chem., August 11, 2000; 275(33): 25672 - 25680. [Abstract] [Full Text] [PDF]
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B. C. Low, K. T. Seow, and G. R. Guy The BNIP-2 and Cdc42GAP Homology Domain of BNIP-2 Mediates Its Homophilic Association and Heterophilic Interaction with Cdc42GAP J. Biol. Chem., November 22, 2000; 275(48): 37742 - 37751. [Abstract] [Full Text] [PDF]
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G. Faulkner, A. Pallavicini, A. Comelli, M. Salamon, G. Bortoletto, C. Ievolella, S. Trevisan, S. Kojic', F. Dalla Vecchia, P. Laveder, et al. FATZ, a Filamin-, Actinin-, and Telethonin-binding Protein of the Z-disc of Skeletal Muscle J. Biol. Chem., December 22, 2000; 275(52): 41234 - 41242. [Abstract] [Full Text] [PDF]
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V. Gervais, D. Busso, E. Wasielewski, A. Poterszman, J.-M. Egly, J.-C. Thierry, and B. Kieffer Solution Structure of the N-terminal Domain of the Human TFIIH MAT1 Subunit. NEW INSIGHTS INTO THE RING FINGER FAMILY J. Biol. Chem., March 2, 2001; 276(10): 7457 - 7464. [Abstract] [Full Text] [PDF]
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