BLAST domain database searches

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... 

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. 

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). 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

ProDom [20,21] is a collection of protein domain families automatically derived from the Swiss-Prot and TrEMBL databases using a novel approach based on recursive PSI-BLAST searches. 

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