Nucleic Acids Research, 2003, Vol. 31, No. 1 383-387
© 2003 Oxford University Press
CDD: a curated Entrez database of conserved domain alignments
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
*To whom correspondence should be addressed. Tel: +1 3014354919; Fax: +1 3014809241; Email: bauer{at}ncbi.nlm.nih.gov
ABSTRACT
The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE®. This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein–protein queries submitted to BLAST® at http://www.ncbi.nlm.nih.gov/BLAST.
CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate ‘columns’ corresponding to functional sites conserved among family members.
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|
|
|
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 A Warrington, A R Vieira, K Christensen, I M Orioli, E E Castilla, P A Romitti, and J C Murray Genetic evidence for the role of loci at 19q13 in cleft lip and palate. J. Med. Genet., June 1, 2006; 43(6): e26 - e26. [Abstract] [Full Text] [PDF]
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|
|
|
|
 |
|
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|
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|
|
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D. J. Begun and H. A. Lindfors Rapid Evolution of Genomic Acp Complement in the melanogaster Subgroup of Drosophila Mol. Biol. Evol., October 1, 2005; 22(10): 2010 - 2021. [Abstract] [Full Text] [PDF]
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 A. Seitz, D. Gourevitch, X.-M. Zhang, L. Clark, P. Chen, M. Kragol, N. Levenkova, J. Rux, S. Samulewicz, and E. Heber-Katz Sense and antisense transcripts of the apolipoprotein E gene in normal and ApoE knockout mice, their expression after spinal cord injury and corresponding human transcripts Hum. Mol. Genet., September 15, 2005; 14(18): 2661 - 2670. [Abstract] [Full Text] [PDF]
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E. G. Matson, M. G. Thompson, S. B. Humphrey, R. L. Zuerner, and T. B. Stanton Identification of Genes of VSH-1, a Prophage-Like Gene Transfer Agent of Brachyspira hyodysenteriae J. Bacteriol., September 1, 2005; 187(17): 5885 - 5892. [Abstract] [Full Text] [PDF]
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K. Pollmann, J. Raff, M. Schnorpfeil, G. Radeva, and S. Selenska-Pobell Novel surface layer protein genes in Bacillus sphaericus associated with unusual insertion elements Microbiology, September 1, 2005; 151(9): 2961 - 2973. [Abstract] [Full Text] [PDF]
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D. Elleder, V. Stepanets, D. C. Melder, F. Senigl, J. Geryk, P. Pajer, J. Plachy, J. Hejnar, J. Svoboda, and M. J. Federspiel The Receptor for the Subgroup C Avian Sarcoma and Leukosis Viruses, Tvc, Is Related to Mammalian Butyrophilins, Members of the Immunoglobulin Superfamily J. Virol., August 15, 2005; 79(16): 10408 - 10419. [Abstract] [Full Text] [PDF]
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K.-W. Huh, J. DeMasi, H. Ogawa, Y. Nakatani, P. M. Howley, and K. Munger Association of the human papillomavirus type 16 E7 oncoprotein with the 600-kDa retinoblastoma protein-associated factor, p600 PNAS, August 9, 2005; 102(32): 11492 - 11497. [Abstract] [Full Text] [PDF]
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M. Yoshida, K. Igarashi, M. Wada, S. Kaneko, N. Suzuki, H. Matsumura, N. Nakamura, H. Ohno, and M. Samejima Characterization of Carbohydrate-Binding Cytochrome b562 from the White-Rot Fungus Phanerochaete chrysosporium Appl. Envir. Microbiol., August 1, 2005; 71(8): 4548 - 4555. [Abstract] [Full Text] [PDF]
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A. Calderon-Flores, G. Du Pont, A. Huerta-Saquero, H. Merchant-Larios, L. Servin-Gonzalez, and S. Duran The Stringent Response Is Required for Amino Acid and Nitrate Utilization, Nod Factor Regulation, Nodulation, and Nitrogen Fixation in Rhizobium etli J. Bacteriol., August 1, 2005; 187(15): 5075 - 5083. [Abstract] [Full Text] [PDF]
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J. Xu, E. Wan, C.-J. Kim, H. G. Floss, and T. Mahmud Identification of tailoring genes involved in the modification of the polyketide backbone of rifamycin B by Amycolatopsis mediterranei S699 Microbiology, August 1, 2005; 151(8): 2515 - 2528. [Abstract] [Full Text] [PDF]
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 K. K. Kojima and H. Fujiwara An extraordinary retrotransposon family encoding dual endonucleases Genome Res., August 1, 2005; 15(8): 1106 - 1117. [Abstract] [Full Text] [PDF]
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P. A. Harries, A. Pan, and R. S. Quatrano Actin-Related Protein2/3 Complex Component ARPC1 Is Required for Proper Cell Morphogenesis and Polarized Cell Growth in Physcomitrella patens PLANT CELL, August 1, 2005; 17(8): 2327 - 2339. [Abstract] [Full Text] [PDF]
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H. M. Li, D. Rotter, S. A. Bonos, W. A. Meyer, and F. C. Belanger Identification of a Gene in the Process of Being Lost from the Genus Agrostis Plant Physiology, August 1, 2005; 138(4): 2386 - 2395. [Abstract] [Full Text] [PDF]
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J. R. Chandler, A. R. Flynn, E. M. Bryan, and G. M. Dunny Specific Control of Endogenous cCF10 Pheromone by a Conserved Domain of the pCF10-Encoded Regulatory Protein PrgY in Enterococcus faecalis J. Bacteriol., July 15, 2005; 187(14): 4830 - 4843. [Abstract] [Full Text] [PDF]
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X. Xiang, L. Chen, X. Huang, Y. Luo, Q. She, and L. Huang Sulfolobus tengchongensis Spindle-Shaped Virus STSV1: Virus-Host Interactions and Genomic Features J. Virol., July 15, 2005; 79(14): 8677 - 8686. [Abstract] [Full Text] [PDF]
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 J. A. Covi and S. C. Hand V-ATPase expression during development of Artemia franciscana embryos: potential role for proton gradients in anoxia signaling J. Exp. Biol., July 15, 2005; 208(14): 2783 - 2798. [Abstract] [Full Text] [PDF]
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 S. Sumanas, T. Jorniak, and S. Lin Identification of novel vascular endothelial-specific genes by the microarray analysis of the zebrafish cloche mutants Blood, July 15, 2005; 106(2): 534 - 541. [Abstract] [Full Text] [PDF]
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S. Schild, A.-K. Lamprecht, and J. Reidl Molecular and Functional Characterization of O Antigen Transfer in Vibrio cholerae J. Biol. Chem., July 8, 2005; 280(27): 25936 - 25947. [Abstract] [Full Text] [PDF]
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 H. Fraimow, C. Knob, I. A. Herrero, and R. Patel Putative VanRS-Like Two-Component Regulatory System Associated with the Inducible Glycopeptide Resistance Cluster of Paenibacillus popilliae Antimicrob. Agents Chemother., July 1, 2005; 49(7): 2625 - 2633. [Abstract] [Full Text] [PDF]
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L. M. C. Hall, S. C. Fawell, X. Shi, M.-C. Faray-Kele, J. Aduse-Opoku, R. A. Whiley, and M. A. Curtis Sequence Diversity and Antigenic Variation at the rag Locus of Porphyromonas gingivalis Infect. Immun., July 1, 2005; 73(7): 4253 - 4262. [Abstract] [Full Text] [PDF]
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W. Zhang and L. Shi Distribution and evolution of multiple-step phosphorelay in prokaryotes: lateral domain recruitment involved in the formation of hybrid-type histidine kinases Microbiology, July 1, 2005; 151(7): 2159 - 2173. [Abstract] [Full Text] [PDF]
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E. J. Alm, K. H. Huang, M. N. Price, R. P. Koche, K. Keller, I. L. Dubchak, and A. P. Arkin The MicrobesOnline Web site for comparative genomics Genome Res., July 1, 2005; 15(7): 1015 - 1022. [Abstract] [Full Text] [PDF]
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M. Novatchkova, M. Wildpaner, D. Schweizer, and F. Eisenhaber PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets Nucleic Acids Res., July 1, 2005; 33(suppl_2): W121 - W125. [Abstract] [Full Text] [PDF]
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A. L. Tek, J. Song, J. Macas, and J. Jiang Sobo, a Recently Amplified Satellite Repeat of Potato, and Its Implications for the Origin of Tandemly Repeated Sequences Genetics, July 1, 2005; 170(3): 1231 - 1238. [Abstract] [Full Text] [PDF]
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N. A. Stover, A. R. O. Cavalcanti, A. J. Li, B. C. Richardson, and L. F. Landweber Reciprocal Fusions of Two Genes in the Formaldehyde Detoxification Pathway in Ciliates and Diatoms Mol. Biol. Evol., July 1, 2005; 22(7): 1539 - 1542. [Abstract] [Full Text] [PDF]
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V. Anantharaman and L. Aravind MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems Bioinformatics, June 15, 2005; 21(12): 2805 - 2811. [Abstract] [Full Text] [PDF]
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H. K. Saini and D. Fischer Meta-DP: domain prediction meta-server Bioinformatics, June 15, 2005; 21(12): 2917 - 2920. [Abstract] [Full Text] [PDF]
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