Databases domain searches

There are many different domain database resources, each with their own priorities and strengths. There is currently no effective way to search them all with a single query. Several should be tested to get the most complete results possible. The Interpro collaboration should facilitate the creation of methods to query all the major domain databases in a single action. 

Fig. 4. Example of output from the seg program (Wootton, 1994). The seg program was run with default parameters on the SWISS-PROT sequence PSPDHUMAN. (A) Tree output format from seg. Lower case sequence on the left is low complexity, whereas the sequence on the right is high complexity. Note that only the regions between residues 13 and 47 and residues 152 and 375 are large enough to contain protein domains. (B) The second output from seg shows the regions of low complexity masked with Xs this sequence is ready for database searching.

A domain family that is considerably expanded in nematodes, relative to vertebrates, is the zona pellucida (ZP) domain (Bork and Sander, 1992). In database searches this domain was found in C. elegans cuticlin-1 (cut-1), a component of the nematode cuticle (Sebastiano et al., 1991), and 33 other C. elegans proteins (Table II). On the basis of disulfide-linked domains that accompany the ZP domain in these proteins, it is likely that they localize to the worm s extracellular matrix. Indeed, it is possible that most of these proteins are components of the worm cuticle. The cuticle structure is the multilayered elastic exoskeleton that determines the worm s body shape. Although vertebrates lack an equivalent... 

Correlations in the co-occurrence of domains can assist in the identification of distant members of a protein family that are not detected with significance using standard database searching methods. In all known examples of proteins with Cl and CNH domains, for example, there is an intervening PH domain (Schultz et al., 1998). The only exception to... 

Another important aspect of structure prediction using PSSMs is the careful determination of the boundaries of distinct domains whose sequences are used as starting points to construct PSSMs. In iterative database searches, this is critical to avoid inclusion of more than one domain, which results in explosion of an iterative search instead of convergence. Using well-defined domain sequences is particularly important in the analysis of small binding domains that frequently are overlooked if combined with larger, usually enzymatic domains. 

When a novel homology domain has been discovered, it is possible to store the corresponding domain descriptor (profile or HMM) in a number of dedicated domain databases, which can be used to analyze newly identified sequences for their domain content [9, 10]. Several competing domain- and motif-databases exist, including PROSITE, PFAM, SMART, and Superfam, which contain descriptors for most, if not all, of the known domains involved in the ubiquitin system [11-14]. Recently, a new meta-database named INTERPRO has been established, which tries to combine the descriptors of several domain databases under a single user interface [15]. Pointers to the very useful search engines of the domain databases are provided in Table 12.1. 

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. 

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). 

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