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Conserved Domain Database

RefSeq (Reference Sequences) e CDD (Conserved Domain Database)... [Pg.498]

A variety of databases and online tools exist to facilitate searches for protein motifs (Table 6). The most comprehensive resource for the detection of large protein motifs is the Conserved Domain Database (CDD) provided by NCBI. The CDD includes all data present in the SMART and PFAM databases, along with some manually curated entries. All protein-protein BLAST... [Pg.522]

Automatic CDD search. When a protein-protein BLAST search in ran, the query protein sequence is also searched against the conserved domains database. The presence of a conserved domain in the protein is reported on the page with the request ID before you format the page. For example, for the blastp problem 1, the query protein contains an amino transferase 1 2 conserved domain indicated by the red bar below the query line seen in Fig. 16. Click on the red bar to accessthe conserved domain database and determine the amino acid positions of the domain. [Pg.173]

Manual CDD search. A protein query can be also manually searched against the conserved domain database. The option is provided under the Protein panel at the Search the conserved domain database (rpsblast) link. Perform this searchfor the protein accession number NP 032294 from the Genomes problem 1 (Fig. 19). [Pg.174]

Marchler-Bauer, A., J. B. Anderson, P F. Cherukuri, C. DeWeese-Scott, L. Y. Geer, M. Gwadz, S. He, et al. 2005. CDD A Conserved Domain Database for protein classification. Nucleic Acids Res 33, Database Issue D192-6. [Pg.37]

National Center for Biotechnology Information (NCBI) Stephen Bryant Emphasis on conserved structure domains with linked database (Conserved Domain Database CDD) and search service http //www.ncbi.nlm.nih.gov/Structure/RESEARCH/ res.html... [Pg.168]

Identifying domains NCBI conserved domain database http // www.ncbi.nlm.nih.gov/Structure/cdd/... [Pg.28]

Recently, NCBI introduced a new search service aimed at identifying conserved domains within a protein sequence. The source database for these searches is called the Conserved Domain Database or CDD. This is a secondary database, with entries... [Pg.262]

Although not comprehensive as of this writing, SMART seems to be the most advanced of these systems, combining high sensitivity of domain detection with acciuacy, high speed, and extremely informative presentation of domain architectures. Rapid searches for protein domains, based on a modification of the PSl-BLAST program is now available through the Conserved Domains Database (CDD) at NCBI (cf. Chapter 11). [Pg.373]

Labes M, Puhler A, Simon R (1990) A new family of RSFlOlO-derived expression and lac-fusion broad-host-range vectors for gram-negative bacteria. Gene 89(l) 37-46 Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Bryant SH (2011) CDD a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39(Database issue) D225-229... [Pg.221]

ExPASy (Expert Protein Analysis System, www.expasy.ch) or the National Centre for Biotechnology Information (NCBI, www.ncbi.nlm.gov) websites. Both websites provide bioinformatics tools, links to sequence databases and extensive bibliographic resources. As an example of the wealth of information available on individual enzymes, at the time of writing a search based on nitrilase in the Entrez protein section of NCBI will recover more than 10000 references to nitrilase enzyme amino acid sequences. These can be rapidly screened online by organism, and the individual entries will have links to amino acid and gene sequence, relevant literature and information on protein features (such as conserved domains). [Pg.90]

Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. CDD a curated Entrez database of conserved domain alignments. Nucleic Acids Res 2003 31 383-387. [Pg.554]

Marchler-Bauer A, Panchenko AR, Shoemaker BA et al (2002) CDD a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 30 281-283... [Pg.174]

The data are collected daily from a number of sources, including the National Center for Biotechnology Information (NCBI) and Gene Ontology (GO) Consortium. The warehouse includes sequences, structures, and complete genomes from Gen-Bank as well as annotation links such as NCBI taxon database terms, redundant sequences, sequence neighbors, conserved domains, Online Mendehan Inheritance in Man identifiers, GO terms, LocusLink identifiers, and PubMed links. [Pg.393]

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See also in sourсe #XX -- [ Pg.67 ]



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Conserved domains

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