Nucleic Acids Research, 2002, Vol. 30, No. 1 281-283
© 2002 Oxford University Press
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. It has been populated with alignment data from the public collections Pfam and SMART, as well as with contributions from colleagues at NCBI. The current version of CDD (v.1.54) contains 3693 such models. CDD alignments are linked to protein sequence and structure data in Entrez. The molecular structure viewer Cn3D serves as a tool to interactively visualize alignments and three-dimensional structure, and to link three-dimensional residue coordinates to descriptions of evolutionary conservation. CDD can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. Protein query sequences may be compared against databases of position-specific score matrices derived from alignments in CDD, using a service named CD-Search, which can be found at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search runs reverse-position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm. CD-Search is run by default for protein–protein queries submitted to NCBI’s BLAST service at http://www.ncbi.nlm.nih.gov/BLAST.
* To whom correspondence should be addressed. Tel: +1 301 435 4919; Fax: +1 301 480 9241; Email: bauer{at}ncbi.nlm.nih.gov
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H. A. van den Burg, N. Westerink, K.-J. Francoijs, R. Roth, E. Woestenenk, S. Boeren, P. J. G. M. de Wit, M. H. A. J. Joosten, and J. Vervoort Natural Disulfide Bond-disrupted Mutants of AVR4 of the Tomato Pathogen Cladosporium fulvum Are Sensitive to Proteolysis, Circumvent Cf-4-mediated Resistance, but Retain Their Chitin Binding Ability J. Biol. Chem., July 18, 2003; 278(30): 27340 - 27346. [Abstract] [Full Text] [PDF]
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E. A. Worthey, S. Martinez-Calvillo, A. Schnaufer, G. Aggarwal, J. Cawthra, G. Fazelinia, C. Fong, G. Fu, M. Hassebrock, G. Hixson, et al. Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene Nucleic Acids Res., July 15, 2003; 31(14): 4201 - 4210. [Abstract] [Full Text] [PDF]
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N. V. Bykova, A. Stensballe, H. Egsgaard, O. N. Jensen, and I. M. Moller Phosphorylation of Formate Dehydrogenase in Potato Tuber Mitochondria J. Biol. Chem., July 3, 2003; 278(28): 26021 - 26030. [Abstract] [Full Text] [PDF]
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G. Yadav, R. S. Gokhale, and D. Mohanty SEARCHPKS: a program for detection and analysis of polyketide synthase domains Nucleic Acids Res., July 1, 2003; 31(13): 3654 - 3658. [Abstract] [Full Text] [PDF]
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M. Madson, C. Dunand, X. Li, R. Verma, G. F. Vanzin, J. Caplan, D. A. Shoue, N. C. Carpita, and W.-D. Reiter The MUR3 Gene of Arabidopsis Encodes a Xyloglucan Galactosyltransferase That Is Evolutionarily Related to Animal Exostosins PLANT CELL, July 1, 2003; 15(7): 1662 - 1670. [Abstract] [Full Text] [PDF]
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A. Androutsellis-Theotokis, N. R. Goldberg, K. Ueda, T. Beppu, M. L. Beckman, S. Das, J. A. Javitch, and G. Rudnick Characterization of a Functional Bacterial Homologue of Sodium-dependent Neurotransmitter Transporters J. Biol. Chem., April 4, 2003; 278(15): 12703 - 12709. [Abstract] [Full Text] [PDF]
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