Conserved Domain Search (CD Search) results now show domain architecture information and other annotations that further characterize predicted domain and protein function. These include links to PubMed, Gene Ontology (GO) terms, Enzyme Commission (EC) numbers, and the SPARCLE Domain Architecture Viewer. You can use these links on the results to find literature (PubMed), assign biological roles and protein function (GO and EC), and find proteins with the same domain architecture (Domain Architecture Viewer). These annotations are currently available for a limited number of architectures, but we will continue to add them as part of our curation effort.
Figure 1 shows the results of an example CD Search showing these new links. Note that you can use the GO and EC information provided to retrieve protein models with these annotations from the Protein Family Models database, for example GO:0030246[GOTermId] — molecular function carbohydrate binding or 2.7.11.1[ECNumber] — non-specific serine/threonine protein kinase.
Figure 1. Conserved Domain Database search results for a hypothetical protein (XP_007132600.1) from the common bean (Phaseolus vulgaris). The results classify the protein as a plant receptor-like protein kinase. The results also show the EC number and the GO terms associated with this domain architecture, a link to a PubMed citation for the protein family (receptor-like protein kinases), and a link to the Domain Architecture Viewer for G-type lectin S-receptor-like serine/threonine-protein kinases. The Domain Architecture Viewer shows other proteins from the NCBI databases with the same domain architecture (order, number and types of domains).
You can also see GO, EC, and PubMed annotations on BATCH CD-Search results in the results browser when you mouse over the query title (Figure 2).
Figure 2. A portion of the results from Batch CD Search in the Results browser. The protein classification, links to GO Terms, EC Number and PubMed are for the selected query (XP_007132600.1) and appear on mouse-over of the query identifier string.
CD Search is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms.
Join our mailing list to keep up to date with CD Search and other CGR news.
Amazing