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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. N.I. Pang, K. Lin, M. A. Wouters, J. Heringa, and R. A. George Identifying foldable regions in protein sequence from the hydrophobic signal Nucleic Acids Res., February 2, 2008; 36(2): 578 - 588. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Moses, M. E. Liku, J. J. Li, and R. Durbin Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites PNAS, November 6, 2007; 104(45): 17713 - 17718. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bettegowda, J. Yao, A. Sen, Q. Li, K.-B. Lee, Y. Kobayashi, O. V. Patel, P. M. Coussens, J. J. Ireland, and G. W. Smith JY-1, an oocyte-specific gene, regulates granulosa cell function and early embryonic development in cattle PNAS, November 6, 2007; 104(45): 17602 - 17607. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Paul, K. Gable, and T. M. Dunn A Six-membrane-spanning Topology for Yeast and Arabidopsis Tsc13p, the Enoyl Reductases of the Microsomal Fatty Acid Elongating System J. Biol. Chem., June 29, 2007; 282(26): 19237 - 19246. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Fujishima, M. Komasa, S. Kitamura, H. Suzuki, M. Tomita, and A. Kanai Proteome-Wide Prediction of Novel DNA/RNA-Binding Proteins Using Amino Acid Composition and Periodicity in the Hyperthermophilic Archaeon Pyrococcus furiosus DNA Res, June 15, 2007; (2007) dsm011v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Salamat-Miller, J. Fang, C. W. Seidel, Y. Assenov, M. Albrecht, and C. R. Middaugh A Network-based Analysis of Polyanion-binding Proteins Utilizing Human Protein Arrays J. Biol. Chem., April 6, 2007; 282(14): 10153 - 10163. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. J. Lingle Gating Rings Formed by RCK Domains: Keys to Gate Opening J. Gen. Physiol., February 2, 2007; 129(2): 101 - 107. [Full Text] [PDF]
|
|
|
|
|
|
P. Kowal, A. M. Gurtan, P. Stuckert, A. D. D'Andrea, and T. Ellenberger Structural Determinants of Human FANCF Protein That Function in the Assembly of a DNA Damage Signaling Complex J. Biol. Chem., January 19, 2007; 282(3): 2047 - 2055. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Y. Galperin The Molecular Biology Database Collection: 2007 update Nucleic Acids Res., January 12, 2007; 35(suppl_1): D3 - D4. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Aurrecoechea, M. Heiges, H. Wang, Z. Wang, S. Fischer, P. Rhodes, J. Miller, E. Kraemer, C. J. Stoeckert Jr., D. S. Roos, et al. ApiDB: integrated resources for the apicomplexan bioinformatics resource center Nucleic Acids Res., January 12, 2007; 35(suppl_1): D427 - D430. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Lanie, W.-L. Ng, K. M. Kazmierczak, T. M. Andrzejewski, T. M. Davidsen, K. J. Wayne, H. Tettelin, J. I. Glass, and M. E. Winkler Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6 J. Bacteriol., January 1, 2007; 189(1): 38 - 51. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Talla, C. Narayanan, N. Srinivasan, and D. Balasubramanian Mutation Causing Self-Aggregation in Human {gamma}C-Crystallin Leading to Congenital Cataract Invest. Ophthalmol. Vis. Sci., December 1, 2006; 47(12): 5212 - 5217. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Ouyang and R. Isaacson Identification and Characterization of a Novel ABC Iron Transport System, fit, in Escherichia coli Infect. Immun., December 1, 2006; 74(12): 6949 - 6956. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. L. Maeder, I. Anderson, T. S. Brettin, D. C. Bruce, P. Gilna, C. S. Han, A. Lapidus, W. W. Metcalf, E. Saunders, R. Tapia, et al. The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes J. Bacteriol., November 15, 2006; 188(22): 7922 - 7931. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Louvel, S. Bommezzadri, N. Zidane, C. Boursaux-Eude, S. Creno, A. Magnier, Z. Rouy, C. Medigue, I. S. Girons, C. Bouchier, et al. Comparative and Functional Genomic Analyses of Iron Transport and Regulation in Leptospira spp. J. Bacteriol., November 15, 2006; 188(22): 7893 - 7904. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Billion, R. Ghai, T. Chakraborty, and T. Hain Augur--a computational pipeline for whole genome microbial surface protein prediction and classification Bioinformatics, November 15, 2006; 22(22): 2819 - 2820. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. W. Buchko, S. Ni, H. Robinson, E. A. Welsh, H. B. Pakrasi, and M. A. Kennedy Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142. Protein Sci., November 1, 2006; 15(11): 2579 - 2595. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. S. Goldman, W. C. Nierman, D. Kaiser, S. C. Slater, A. S. Durkin, J. A. Eisen, C. M. Ronning, W. B. Barbazuk, M. Blanchard, C. Field, et al. Evolution of sensory complexity recorded in a myxobacterial genome PNAS, October 10, 2006; 103(41): 15200 - 15205. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. B. Cannon, L. Sterck, S. Rombauts, S. Sato, F. Cheung, J. Gouzy, X. Wang, J. Mudge, J. Vasdewani, T. Schiex, et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes PNAS, October 3, 2006; 103(40): 14959 - 14964. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Nakayama, M. Iida, H. Koseki, and O. Ohara A gene-targeting approach for functional characterization of KIAA genes encoding extremely large proteins FASEB J, August 1, 2006; 20(10): 1718 - 1720. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gough Genomic scale sub-family assignment of protein domains Nucleic Acids Res., July 28, 2006; 34(13): 3625 - 3633. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. P. Duffy, A. M. Young, B. Morin, C. J. Lucarotti, B. F. Koop, and D. B. Levin Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome J. Virol., July 15, 2006; 80(14): 6952 - 6963. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Lozada-Chavez, S. C. Janga, and J. Collado-Vides Bacterial regulatory networks are extremely flexible in evolution Nucleic Acids Res., July 13, 2006; 34(12): 3434 - 3445. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Kaur, M. Pan, M. Meislin, M. T. Facciotti, R. El-Gewely, and N. S. Baliga A systems view of haloarchaeal strategies to withstand stress from transition metals Genome Res., July 1, 2006; 16(7): 841 - 854. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. B. Yaffe "Bits" and Pieces Sci. Signal., June 20, 2006; 2006(340): pe28 - pe28. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Wang, Y. Hu, M. T. Overgaard, F. V. Karginov, O. C. Uhlenbeck, and D. B. McKay The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold RNA, June 1, 2006; 12(6): 959 - 967. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Staub and D. Rotin Role of Ubiquitylation in Cellular Membrane Transport Physiol Rev, April 1, 2006; 86(2): 669 - 707. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. L. Goldstein, D. Glossip, S. Nayak, and K. Kornfeld The CRAL/TRIO and GOLD Domain Protein CGR-1 Promotes Induction of Vulval Cell Fates in Caenorhabditis elegans and Interacts Genetically With the Ras Signaling Pathway Genetics, February 1, 2006; 172(2): 929 - 942. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Takac, M. A. Nunn, J. Meszaros, O. Pechanova, N. Vrbjar, P. Vlasakova, M. Kozanek, M. Kazimirova, G. Hart, P. A. Nuttall, et al. Vasotab, a vasoactive peptide from horse fly Hybomitra bimaculata (Diptera, Tabanidae) salivary glands J. Exp. Biol., January 15, 2006; 209(2): 343 - 352. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Grillari, P. Ajuh, G. Stadler, M. Loscher, R. Voglauer, W. Ernst, J. Chusainow, F. Eisenhaber, M. Pokar, K. Fortschegger, et al. SNEV is an evolutionarily conserved splicing factor whose oligomerization is necessary for spliceosome assembly Nucleic Acids Res., December 6, 2005; 33(21): 6868 - 6883. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Mutoh, T. Suzuki, K. Hasegawa, Y. Nakazawa, H. Kouguchi, Y. Sagane, K. Niwa, T. Watanabe, and T. Ohyama Four molecules of the 33 kDa haemagglutinin component of the Clostridium botulinum serotype C and D toxin complexes are required to aggregate erythrocytes Microbiology, December 1, 2005; 151(12): 3847 - 3858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Magen and G. Ast The importance of being divisible by three in alternative splicing Nucleic Acids Res., September 28, 2005; 33(17): 5574 - 5582. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Kang and D. C. Gross Characterization of a Resistance-Nodulation-Cell Division Transporter System Associated with the syr-syp Genomic Island of Pseudomonas syringae pv. syringae Appl. Envir. Microbiol., September 1, 2005; 71(9): 5056 - 5065. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Bourhy, L. Frangeul, E. Couve, P. Glaser, I. Saint Girons, and M. Picardeau Complete Nucleotide Sequence of the LE1 Prophage from the Spirochete Leptospira biflexa and Characterization of Its Replication and Partition Functions J. Bacteriol., June 15, 2005; 187(12): 3931 - 3940. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. K. Saini and D. Fischer Meta-DP: domain prediction meta-server Bioinformatics, June 15, 2005; 21(12): 2917 - 2920. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Brocchieri and S. Karlin Protein length in eukaryotic and prokaryotic proteomes Nucleic Acids Res., June 10, 2005; 33(10): 3390 - 3400. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. L. Ramos, M. Martinez-Bueno, A. J. Molina-Henares, W. Teran, K. Watanabe, X. Zhang, M. T. Gallegos, R. Brennan, and R. Tobes The TetR Family of Transcriptional Repressors Microbiol. Mol. Biol. Rev., June 1, 2005; 69(2): 326 - 356. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gough Convergent evolution of domain architectures (is rare) Bioinformatics, April 15, 2005; 21(8): 1464 - 1471. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Ferron, C. Rancurel, S. Longhi, C. Cambillau, B. Henrissat, and B. Canard VaZyMolO: a tool to define and classify modularity in viral proteins J. Gen. Virol., March 1, 2005; 86(3): 743 - 749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Dziejman, D. Serruto, V. C. Tam, D. Sturtevant, P. Diraphat, S. M. Faruque, M. H. Rahman, J. F. Heidelberg, J. Decker, L. Li, et al. Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system PNAS, March 1, 2005; 102(9): 3465 - 3470. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Porto, H. E. Roman, M. Vendruscolo, and U. Bastolla Prediction of Site-Specific Amino Acid Distributions and Limits of Divergent Evolutionary Changes in Protein Sequences Mol. Biol. Evol., March 1, 2005; 22(3): 630 - 638. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Nunn, A. Sharma, G. C. Paesen, S. Adamson, O. Lissina, A. C. Willis, and P. A. Nuttall Complement Inhibitor of C5 Activation from the Soft Tick Ornithodoros moubata J. Immunol., February 15, 2005; 174(4): 2084 - 2091. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Marchin, P. T. Kelly, and J. Fang Tracker: continuous HMMER and BLAST searching Bioinformatics, February 1, 2005; 21(3): 388 - 389. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Takayama, C. Wang, and G. S. Besra Pathway to Synthesis and Processing of Mycolic Acids in Mycobacterium tuberculosis Clin. Microbiol. Rev., January 1, 2005; 18(1): 81 - 101. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. C. Park, K.-H. Song, H. K. Chung, H. Kim, D. W. Kim, J. H. Song, E. S. Hwang, H. S. Jung, S.-H. Park, I. Bae, et al. CR6-Interacting Factor 1 Interacts with Orphan Nuclear Receptor Nur77 and Inhibits Its Transactivation Mol. Endocrinol., January 1, 2005; 19(1): 12 - 24. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. S. Baliga, R. Bonneau, M. T. Facciotti, M. Pan, G. Glusman, E. W. Deutsch, P. Shannon, Y. Chiu, R. S. Weng, R. R. Gan, et al. Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea Genome Res., November 1, 2004; 14(11): 2221 - 2234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. S. Janssen, R. S. Phillips, C. M. R. Turner, and M. P. Barrett Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites Nucleic Acids Res., October 26, 2004; 32(19): 5712 - 5720. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. V. Lunin, Y. Li, J. D. Schrag, P. Iannuzzi, M. Cygler, and A. Matte Crystal Structures of Escherichia coli ATP-Dependent Glucokinase and Its Complex with Glucose J. Bacteriol., October 15, 2004; 186(20): 6915 - 6927. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. G. Valenzuela, M. Garfield, E. D. Rowton, and V. M. Pham Identification of the most abundant secreted proteins from the salivary glands of the sand fly Lutzomyia longipalpis, vector of Leishmania chagasi J. Exp. Biol., October 1, 2004; 207(21): 3717 - 3729. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. C. Nierman, D. DeShazer, H. S. Kim, H. Tettelin, K. E. Nelson, T. Feldblyum, R. L. Ulrich, C. M. Ronning, L. M. Brinkac, S. C. Daugherty, et al. From the Cover: Structural flexibility in the Burkholderia mallei genome PNAS, September 28, 2004; 101(39): 14246 - 14251. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Shan, H. Xu, X. Shi, Y. Yu, H. Yao, X. Zhang, Y. Bai, C. Gao, P. E. J. Saris, and M. Qiao Identification of two new genes involved in twitching motility in Pseudomonas aeruginosa Microbiology, August 1, 2004; 150(8): 2653 - 2661. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W.-G. Qiu, N. Schisler, and A. Stoltzfus The Evolutionary Gain of Spliceosomal Introns: Sequence and Phase Preferences Mol. Biol. Evol., July 1, 2004; 21(7): 1252 - 1263. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. L. Turner, J. C. Waller, B. Vanderbeld, and W. A. Snedden Cloning and Characterization of Two NAD Kinases from Arabidopsis. Identification of a Calmodulin Binding Isoform Plant Physiology, July 1, 2004; 135(3): 1243 - 1255. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Sharma, M. Isogai, T. Yamamoto, K. Sakaguchi, J. Hashimoto, and S. Komatsu A Novel Interaction between Calreticulin and Ubiquitin-Like Nuclear Protein in Rice Plant Cell Physiol., June 15, 2004; 45(6): 684 - 692. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kim, H. Yang, S.-K. Kim, P. A. Reche, R. S. Tirabassi, R. E. Hussey, Y. Chishti, J. G. Rheinwald, T. J. Morehead, T. Zech, et al. Biochemical and Functional Analysis of Smallpox Growth Factor (SPGF) and Anti-SPGF Monoclonal Antibodies J. Biol. Chem., June 11, 2004; 279(24): 25838 - 25848. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Srikumar, L. G. Mikael, P. D. Pawelek, A. Khamessan, B. F. Gibbs, M. Jacques, and J. W. Coulton Molecular cloning of haemoglobin-binding protein HgbA in the outer membrane of Actinobacillus pleuropneumoniae Microbiology, June 1, 2004; 150(6): 1723 - 1734. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. S. Nield, R. D. Willows, A. E. Torda, M. R. Gillings, A. J. Holmes, K.M. H. Nevalainen, H.W. Stokes, and B. C. Mabbutt New enzymes from environmental cassette arrays: Functional attributes of a phosphotransferase and an RNA-methyltransferase Protein Sci., June 1, 2004; 13(6): 1651 - 1659. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. S. Baliga, S. J. Bjork, R. Bonneau, M. Pan, C. Iloanusi, M. C.H. Kottemann, L. Hood, and J. DiRuggiero Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1 Genome Res., June 1, 2004; 14(6): 1025 - 1035. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Comfort and R. T. Clubb A Comparative Genome Analysis Identifies Distinct Sorting Pathways in Gram-Positive Bacteria Infect. Immun., May 1, 2004; 72(5): 2710 - 2722. [Abstract] [Full Text] [PDF]
|