CD-Search: protein domain annotations on the fly
Computational Biology Branch, NCBI, National Library of Medicine, NIH, Building 38A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
* To whom correspondence should be addressed. Tel: +1 301 435 4919; Fax: +1 301 480 9241; Email: bauer{at}ncbi.nlm.nih.gov
Received February 19, 2004; Revised and Accepted April 21, 2004
We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST® heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models. Search results are displayed as domain architecture cartoons and pairwise alignments between the query and domain-model consensus sequences. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family. CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi.
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 H. Zhao, A. K. Charnley, Z. Wang, Y. Yin, Z. Li, Y. Li, Y. Cao, G. Peng, and Y. Xia Identification of an Extracellular Acid Trehalase and Its Gene Involved in Fungal Pathogenesis of Metarizium anisopliae. J. Biochem., September 1, 2006; 140(3): 319 - 327. [Abstract] [Full Text] [PDF]
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E. T. Larson, D. Reiter, M. Young, and C. M. Lawrence Structure of A197 from Sulfolobus Turreted Icosahedral Virus: a Crenarchaeal Viral Glycosyltransferase Exhibiting the GT-A Fold. J. Virol., August 1, 2006; 80(15): 7636 - 7644. [Abstract] [Full Text] [PDF]
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 J. H. Thomas Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants Genome Res., August 1, 2006; 16(8): 1017 - 1030. [Abstract] [Full Text] [PDF]
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S. M. Joshi, A. K. Pandey, N. Capite, S. M. Fortune, E. J. Rubin, and C. M. Sassetti Characterization of mycobacterial virulence genes through genetic interaction mapping PNAS, August 1, 2006; 103(31): 11760 - 11765. [Abstract] [Full Text] [PDF]
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G. Prosseda, M. C. Latella, M. Casalino, M. Nicoletti, S. Michienzi, and B. Colonna Plasticity of the Pjunc Promoter of ISEc11, a New Insertion Sequence of the IS1111 Family J. Bacteriol., July 1, 2006; 188(13): 4681 - 4689. [Abstract] [Full Text] [PDF]
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J. Tangrot, L. Wang, B. Kagstrom, and U. H. Sauer FISH--family identification of sequence homologues using structure anchored hidden Markov models. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W10 - W14. [Abstract] [Full Text] [PDF]
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M. Novatchkova, G. Schneider, R. Fritz, F. Eisenhaber, and A. Schleiffer DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W214 - W218. [Abstract] [Full Text] [PDF]
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B. Ganesan, P. Dobrowolski, and B. C. Weimer Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis. Appl. Envir. Microbiol., June 1, 2006; 72(6): 4264 - 4273. [Abstract] [Full Text] [PDF]
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M. Y. Galperin Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol., June 1, 2006; 188(12): 4169 - 4182. [Abstract] [Full Text] [PDF]
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A. Virag and S. D. Harris Functional Characterization of Aspergillus nidulans Homologues of Saccharomyces cerevisiae Spa2 and Bud6 Eukaryot. Cell, June 1, 2006; 5(6): 881 - 895. [Abstract] [Full Text] [PDF]
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S. Xiao, J. Hsieh, R. L. Nugent, D. J. Coughlin, C. A. Fierke, and D. R. Engelke Functional characterization of the conserved amino acids in Pop1p, the largest common protein subunit of yeast RNases P and MRP RNA, June 1, 2006; 12(6): 1023 - 1037. [Abstract] [Full Text] [PDF]
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M. J. Gibbs, V. V. Smeianov, J. L. Steele, P. Upcroft, and B. A. Efimov Two Families of Rep-Like Genes That Probably Originated by Interspecies Recombination Are Represented in Viral, Plasmid, Bacterial, and Parasitic Protozoan Genomes Mol. Biol. Evol., June 1, 2006; 23(6): 1097 - 1100. [Abstract] [Full Text] [PDF]
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D. R. Hoen, K. C. Park, N. Elrouby, Z. Yu, N. Mohabir, R. K. Cowan, and T. E. Bureau Transposon-Mediated Expansion and Diversification of a Family of ULP-like Genes Mol. Biol. Evol., June 1, 2006; 23(6): 1254 - 1268. [Abstract] [Full Text] [PDF]
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C. S. Barry and J. J. Giovannoni From The Cover: Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling PNAS, May 16, 2006; 103(20): 7923 - 7928. [Abstract] [Full Text] [PDF]
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H. Nagasaki, M. Arita, T. Nishizawa, M. Suwa, and O. Gotoh Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns Bioinformatics, May 15, 2006; 22(10): 1211 - 1216. [Abstract] [Full Text] [PDF]
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I. C. Gunesekere, C. M. Kahler, C. S. Ryan, L. A. S. Snyder, N. J. Saunders, J. I. Rood, and J. K. Davies Ecf, an Alternative Sigma Factor from Neisseria gonorrhoeae, Controls Expression of msrAB, Which Encodes Methionine Sulfoxide Reductase. J. Bacteriol., May 1, 2006; 188(10): 3463 - 3469. [Abstract] [Full Text] [PDF]
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 B. T. Poulos, K. F. J. Tang, C. R. Pantoja, J. R. Bonami, and D. V. Lightner Purification and characterization of infectious myonecrosis virus of penaeid shrimp. J. Gen. Virol., April 1, 2006; 87(Pt 4): 987 - 996. [Abstract] [Full Text] [PDF]
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S. Bulgheresi, I. Schabussova, T. Chen, N. P. Mullin, R. M. Maizels, and J. A. Ott A New C-Type Lectin Similar to the Human Immunoreceptor DC-SIGN Mediates Symbiont Acquisition by a Marine Nematode Appl. Envir. Microbiol., April 1, 2006; 72(4): 2950 - 2956. [Abstract] [Full Text] [PDF]
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L. L. Grochowski, H. Xu, and R. H. White Identification of Lactaldehyde Dehydrogenase in Methanocaldococcus jannaschii and Its Involvement in Production of Lactate for F420 Biosynthesis. J. Bacteriol., April 1, 2006; 188(8): 2836 - 2844. [Abstract] [Full Text] [PDF]
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E. Eggenhofer, R. Rachel, M. Haslbeck, and B. Scharf MotD of Sinorhizobium meliloti and Related {alpha}-Proteobacteria Is the Flagellar-Hook-Length Regulator and Therefore Reassigned as FliK J. Bacteriol., March 15, 2006; 188(6): 2144 - 2153. [Abstract] [Full Text] [PDF]
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T. Y. James, P. Srivilai, U. Kues, and R. Vilgalys Evolution of the Bipolar Mating System of the Mushroom Coprinellus disseminatus From Its Tetrapolar Ancestors Involves Loss of Mating-Type-Specific Pheromone Receptor Function Genetics, March 1, 2006; 172(3): 1877 - 1891. [Abstract] [Full Text] [PDF]
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Z. Chen and T. D. Schneider Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands Nucleic Acids Res., February 21, 2006; 34(4): 1133 - 1147. [Abstract] [Full Text] [PDF]
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M. S. Bulmer and R. H. Crozier Variation in Positive Selection in Termite GNBPs and Relish Mol. Biol. Evol., February 1, 2006; 23(2): 317 - 326. [Abstract] [Full Text] [PDF]
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W. F. Fricke, H. Seedorf, A. Henne, M. Kruer, H. Liesegang, R. Hedderich, G. Gottschalk, and R. K. Thauer The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis J. Bacteriol., January 15, 2006; 188(2): 642 - 658. [Abstract] [Full Text] [PDF]
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J.-Y. Zhang, J. Zou, Q. Bao, W.-L. Chen, L. Wang, H. Yang, and C.-C. Zhang A Lithium-Sensitive and Sodium-Tolerant 3'-Phosphoadenosine-5'-Phosphatase Encoded by halA from the Cyanobacterium Arthrospira platensis Is Closely Related to Its Counterparts from Yeasts and Plants Appl. Envir. Microbiol., January 1, 2006; 72(1): 245 - 251. [Abstract] [Full Text] [PDF]
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