Article |
Pfam: clans, web tools and services
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/).
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
L. M. Holland, S. T. O'Donnell, D. A. Ryjenkov, L. Gomelsky, S. R. Slater, P. D. Fey, M. Gomelsky, and J. P. O'Gara A Staphylococcal GGDEF Domain Protein Regulates Biofilm Formation Independently of Cyclic Dimeric GMP J. Bacteriol., August 1, 2008; 190(15): 5178 - 5189. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Forslund and E. L. L. Sonnhammer Predicting protein function from domain content Bioinformatics, August 1, 2008; 24(15): 1681 - 1687. [Abstract] [PDF] |
||||
![]() |
K. Pawlowski Uncharacterized/hypothetical proteins in biomedical 'omics' experiments: is novelty being swept under the carpet? Brief Funct Genomic Proteomic, July 19, 2008; (2008) eln033v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Saini, J. D. Brown, P. D. Aldridge, and C. V. Rao FliZ Is a Posttranslational Activator of FlhD4C2-Dependent Flagellar Gene Expression J. Bacteriol., July 15, 2008; 190(14): 4979 - 4988. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. R. Richards, E. E. Herbert, Y. Park, and H. Goodrich-Blair Xenorhabdus nematophila lrhA Is Necessary for Motility, Lipase Activity, Toxin Expression, and Virulence in Manduca sexta Insects J. Bacteriol., July 15, 2008; 190(14): 4870 - 4879. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Popolo, E. Ragni, C. Carotti, O. Palomares, R. Aardema, J. W. Back, H. L. Dekker, L. J. de Koning, L. de Jong, and C. G. de Koster Disulfide Bond Structure and Domain Organization of Yeast {beta}(1,3)-Glucanosyltransferases Involved in Cell Wall Biogenesis J. Biol. Chem., July 4, 2008; 283(27): 18553 - 18565. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Wada, T. Ando, M. Kiyohara, H. Ashida, M. Kitaoka, M. Yamaguchi, H. Kumagai, T. Katayama, and K. Yamamoto Bifidobacterium bifidum Lacto-N-Biosidase, a Critical Enzyme for the Degradation of Human Milk Oligosaccharides with a Type 1 Structure Appl. Envir. Microbiol., July 1, 2008; 74(13): 3996 - 4004. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. O. Collins, L. Yu, I. Campuzano, S. G. N. Grant, and J. S. Choudhary Phosphoproteomic Analysis of the Mouse Brain Cytosol Reveals a Predominance of Protein Phosphorylation in Regions of Intrinsic Sequence Disorder Mol. Cell. Proteomics, July 1, 2008; 7(7): 1331 - 1348. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Wong and M. A. Ragan MACHOS: Markov clusters of homologous subsequences Bioinformatics, July 1, 2008; 24(13): i77 - i85. [Abstract] [PDF] |
||||
![]() |
A. Stojmirovic, E. M. Gertz, S. F. Altschul, and Y.-K. Yu The effectiveness of position- and composition-specific gap costs for protein similarity searches Bioinformatics, July 1, 2008; 24(13): i15 - i23. [Abstract] [PDF] |
||||
![]() |
Y. Loewenstein, E. Portugaly, M. Fromer, and M. Linial Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space Bioinformatics, July 1, 2008; 24(13): i41 - i49. [Abstract] [PDF] |
||||
![]() |
J. A. Capra and M. Singh Characterization and prediction of residues determining protein functional specificity Bioinformatics, July 1, 2008; 24(13): 1473 - 1480. [Abstract] [PDF] |
||||
![]() |
I. M. Overton, C. A. J. van Niekerk, L. G. Carter, A. Dawson, D. M. A. Martin, S. Cameron, S. A. McMahon, M. F. White, W. N. Hunter, J. H. Naismith, et al. TarO: a target optimisation system for structural biology Nucleic Acids Res., July 1, 2008; 36(suppl_2): W190 - W196. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. E. Tusnady, L. Kalmar, H. Hegyi, P. Tompa, and I. Simon TOPDOM: database of domains and motifs with conservative location in transmembrane proteins Bioinformatics, June 15, 2008; 24(12): 1469 - 1470. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Dumetz, E. Duchaud, S. Claverol, N. Orieux, S. Papillon, D. Lapaillerie, and M. Le Henaff Analysis of the Flavobacterium psychrophilum outer-membrane subproteome and identification of new antigenic targets for vaccine by immunomics Microbiology, June 1, 2008; 154(6): 1793 - 1801. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. A. Anwar, S. Kralj, M. J. E. C. van der Maarel, and L. Dijkhuizen The Probiotic Lactobacillus johnsonii NCC 533 Produces High-Molecular-Mass Inulin from Sucrose by Using an Inulosucrase Enzyme Appl. Envir. Microbiol., June 1, 2008; 74(11): 3426 - 3433. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Li, C. Wu, H. Huang, K. Zhang, J. Gan, and S. S.-C. Li Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach Nucleic Acids Res., June 1, 2008; 36(10): 3263 - 3273. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. M. Reitzel, J. C. Sullivan, N. Traylor-knowles, and J. R. Finnerty Genomic Survey of Candidate Stress-Response Genes in the Estuarine Anemone Nematostella vectensis Biol. Bull., June 1, 2008; 214(3): 233 - 254. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. T.-B. G. Schjoldager, H. R. Maltesen, S. Balmer, L. R. Lund, M. H. Claesson, H. Sjostrom, J. T. Troelsen, and J. Olsen Cellular cross talk in the small intestinal mucosa: postnatal lymphocytic immigration elicits a specific epithelial transcriptional response Am J Physiol Gastrointest Liver Physiol, June 1, 2008; 294(6): G1335 - G1343. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. A. Mihindukulasuriya, G. Wu, J. St. Leger, R. W. Nordhausen, and D. Wang Identification of a Novel Coronavirus from a Beluga Whale by Using a Panviral Microarray J. Virol., May 15, 2008; 82(10): 5084 - 5088. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. E. Loper, M. D. Henkels, B. T. Shaffer, F. A. Valeriote, and H. Gross Isolation and Identification of Rhizoxin Analogs from Pseudomonas fluorescens Pf-5 by Using a Genomic Mining Strategy Appl. Envir. Microbiol., May 15, 2008; 74(10): 3085 - 3093. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Szczesny and A. Lupas Domain annotation of trimeric autotransporter adhesins--daTAA Bioinformatics, May 15, 2008; 24(10): 1251 - 1256. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. E. Elliott, Harjono, and B. J. Howlett Mutation of a Gene in the Fungus Leptosphaeria maculans Allows Increased Frequency of Penetration of Stomatal Apertures of Arabidopsis thaliana Mol Plant, May 9, 2008; (2008) ssn014v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. Suzuki, J. Wada, T. Katayama, S. Fushinobu, T. Wakagi, H. Shoun, H. Sugimoto, A. Tanaka, H. Kumagai, H. Ashida, et al. Structural and Thermodynamic Analyses of Solute-binding Protein from Bifidobacterium longum Specific for Core 1 Disaccharide and Lacto-N-biose I J. Biol. Chem., May 9, 2008; 283(19): 13165 - 13173. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. D. Schrag, S. Jiralerspong, M. Banville, M. L. Jaramillo, and M. D. O'Connor-McCourt The crystal structure and dimerization interface of GADD45{gamma} PNAS, May 6, 2008; 105(18): 6566 - 6571. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. C. Sutcliffe, G. W. Black, and D. J. Harrington Bioinformatic insights into the biosynthesis of the Group B carbohydrate in Streptococcus agalactiae Microbiology, May 1, 2008; 154(5): 1354 - 1363. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. J. Sammut, R. D. Finn, and A. Bateman Pfam 10 years on: 10 000 families and still growing Brief Bioinform, May 1, 2008; 9(3): 210 - 219. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. R. Dyson, R. L. Perera, S. P. Shadbolt, L. Biderman, K. Bromek, N. V. Murzina, and J. McCafferty Identification of soluble protein fragments by gene fragmentation and genetic selection Nucleic Acids Res., May 1, 2008; 36(9): e51 - e51. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Lange, S. Holec, V. Cognat, L. Pieuchot, M. Le Ret, J. Canaday, and D. Gagliardi Degradation of a Polyadenylated rRNA Maturation By-Product Involves One of the Three RRP6-Like Proteins in Arabidopsis thaliana Mol. Cell. Biol., May 1, 2008; 28(9): 3038 - 3044. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. M. Riano-Pachon, L. G. G. Correa, R. Trejos-Espinosa, and B. Mueller-Roeber Green Transcription Factors: A Chlamydomonas Overview Genetics, May 1, 2008; 179(1): 31 - 39. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. Ruiz, L. S. Gronenberg, D. Kahne, and T. J. Silhavy Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli PNAS, April 8, 2008; 105(14): 5537 - 5542. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Hegermann, S. Halbedel, R. Dumke, J. Regula, R. R. Gabdoulline, F. Mayer, J. Stulke, and R. Herrmann The acidic, glutamine-rich Mpn474 protein of Mycoplasma pneumoniae is surface exposed and covers the complete cell Microbiology, April 1, 2008; 154(4): 1185 - 1192. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. A. Rodionov, X. Li, I. A. Rodionova, C. Yang, L. Sorci, E. Dervyn, D. Martynowski, H. Zhang, M. S. Gelfand, and A. L. Osterman Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon Nucleic Acids Res., April 1, 2008; 36(6): 2032 - 2046. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Krause, N. N. Diaz, A. Goesmann, S. Kelley, T. W. Nattkemper, F. Rohwer, R. A. Edwards, and J. Stoye Phylogenetic classification of short environmental DNA fragments Nucleic Acids Res., April 1, 2008; 36(7): 2230 - 2239. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. I. Sadreyev and N. V. Grishin Accurate statistical model of comparison between multiple sequence alignments Nucleic Acids Res., April 1, 2008; 36(7): 2240 - 2248. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. M. Overton, G. Padovani, M. A. Girolami, and G. J. Barton ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction Bioinformatics, April 1, 2008; 24(7): 901 - 907. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. De La Chesnaye, B. Kerr, A. Paredes, H. Merchant-Larios, J. P. Mendez, and S. R. Ojeda Fbxw15/Fbxo12J Is an F-Box Protein-Encoding Gene Selectively Expressed in Oocytes of the Mouse Ovary Biol Reprod, April 1, 2008; 78(4): 714 - 725. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Ruiz-Trillo, A. J. Roger, G. Burger, M. W. Gray, and B. F. Lang A Phylogenomic Investigation into the Origin of Metazoa Mol. Biol. Evol., April 1, 2008; 25(4): 664 - 672. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. J. Pierro, E. L. Powers, and K. E. Olson Genetic Determinants of Sindbis Virus Mosquito Infection Are Associated with a Highly Conserved Alphavirus and Flavivirus Envelope Sequence J. Virol., March 15, 2008; 82(6): 2966 - 2974. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. N. Wass and M. J. E. Sternberg ConFunc--functional annotation in the twilight zone Bioinformatics, March 15, 2008; 24(6): 798 - 806. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. E. JENNEY JR and M. W. W. ADAMS Hydrogenases of the Model Hyperthermophiles Ann. N.Y. Acad. Sci., March 1, 2008; 1125(1): 252 - 266. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. L. Hayes, B. L. Lytle, B. F. Volkman, and F. C. Peterson The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominately unstructured protein Protein Sci., March 1, 2008; 17(3): 571 - 576. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. D. King, E. F. Mulrooney, E. Vinogradov, B. Kneidinger, K. Mead, and J. S. Lam lfnA from Pseudomonas aeruginosa O12 and wbuX from Escherichia coli O145 Encode Membrane-Associated Proteins and Are Required for Expression of 2,6-Dideoxy-2-Acetamidino-L-Galactose in Lipopolysaccharide O Antigen J. Bacteriol., March 1, 2008; 190(5): 1671 - 1679. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. M. Belchik and L. Xun Functions of Flavin Reductase and Quinone Reductase in 2,4,6-Trichlorophenol Degradation by Cupriavidus necator JMP134 J. Bacteriol., March 1, 2008; 190(5): 1615 - 1619. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Geng, J. B. Bruhn, K. F. Nielsen, L. Gram, and R. Belas Genetic Dissection of Tropodithietic Acid Biosynthesis by Marine Roseobacters Appl. Envir. Microbiol., March 1, 2008; 74(5): 1535 - 1545. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. K. Basu, L. Carmel, I. B. Rogozin, and E. V. Koonin Evolution of protein domain promiscuity in eukaryotes Genome Res., March 1, 2008; 18(3): 449 - 461. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. Ohnuma, S. Onaga, K. Murata, T. Taira, and E. Katoh LysM Domains from Pteris ryukyuensis Chitinase-A: A STABILITY STUDY AND CHARACTERIZATION OF THE CHITIN-BINDING SITE J. Biol. Chem., February 22, 2008; 283(8): 5178 - 5187. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. C. Oliver and M. Paetzel Crystal Structure of the Major Periplasmic Domain of the Bacterial Membrane Protein Assembly Facilitator YidC J. Biol. Chem., February 22, 2008; 283(8): 5208 - 5216. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. S. Rangarajan, A. Asinas, A. Proteau, C. Munger, J. Baardsnes, P. Iannuzzi, A. Matte, and M. Cygler Structure of [NiFe] Hydrogenase Maturation Protein HypE from Escherichia coli and Its Interaction with HypF J. Bacteriol., February 15, 2008; 190(4): 1447 - 1458. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Stevenson, M. Dieckelmann, and P. R. Reeves Determination of Glycosyltransferase Specificities for the Escherichia coli O111 O Antigen by a Generic Approach Appl. Envir. Microbiol., February 15, 2008; 74(4): 1294 - 1298. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Michael, G. Trave, C. Ramu, C. Chica, and T. J. Gibson Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation Bioinformatics, February 15, 2008; 24(4): 453 - 457. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. D. Gordon, G. L. Ottaviano, S. E. Connell, G. V. Tobkin, C. H. Son, S. Shterental, and A. M. Gehring Secreted-Protein Response to {sigma}U Activity in Streptomyces coelicolor J. Bacteriol., February 1, 2008; 190(3): 894 - 904. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Forslund, A. Henricson, V. Hollich, and E. L. L. Sonnhammer Domain Tree-Based Analysis of Protein Architecture Evolution Mol. Biol. Evol., February 1, 2008; 25(2): 254 - 264. [Abstract] [Full Text] [PDF] |
||||
![]() |
O. J. Jabado, Y. Liu, S. Conlan, P. L. Quan, H. Hegyi, Y. Lussier, T. Briese, G. Palacios, and W. I. Lipkin Comprehensive viral oligonucleotide probe design using conserved protein regions Nucleic Acids Res., January 17, 2008; 36(1): e3 - e3. [Abstract] [Full Text] [PDF] |
||||
![]() |
X. Shi, S. Wegener-Feldbrugge, S. Huntley, N. Hamann, R. Hedderich, and L. Sogaard-Andersen Bioinformatics and Experimental Analysis of Proteins of Two-Component Systems in Myxococcus xanthus J. Bacteriol., January 15, 2008; 190(2): 613 - 624. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Guettler, M. K. Vartiainen, F. Miralles, B. Larijani, and R. Treisman RPEL Motifs Link the Serum Response Factor Cofactor MAL but Not Myocardin to Rho Signaling via Actin Binding Mol. Cell. Biol., January 15, 2008; 28(2): 732 - 742. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. J. Siezen, M. J. C. Starrenburg, J. Boekhorst, B. Renckens, D. Molenaar, and J. E. T. van Hylckama Vlieg Genome-Scale Genotype-Phenotype Matching of Two Lactococcus lactis Isolates from Plants Identifies Mechanisms of Adaptation to the Plant Niche Appl. Envir. Microbiol., January 15, 2008; 74(2): 424 - 436. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Bashton, I. Nobeli, and J. M. Thornton PROCOGNATE: a cognate ligand domain mapping for enzymes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D618 - D622. [Abstract] [Full Text] [PDF] |
||||
![]() |
|




















