| Conserved Domains and Protein Classification |
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- Use the CD-Search tool to identify conserved domains, or functional units, within a protein query sequence:
- Enter the protein query sequence, either as raw sequence data in FASTA format, or as a GI or Accession.
- Select the database against which you would like to search and use the advanced search options to adjust search sensitivity and display options, if desired, or just use the default settings, then press the "Submit" button.
- The search results will be shown in the default Concise Display, which shows only the top scoring hits for each region of the query sequence. Change to the Full Display if you'd like to see all hits.
- Four types of hits can be present in search results: specific hits, non-specific hits, the superfamily(ies) to which those hits belong, and multi-domain models. Small triangles, when present, indicate amino acids involved in conserved features/sites, such as catalytic and binding sites.
- If CD-Search finds a specific hit, there is a high confidence in the association between the protein query sequence and a conserved domain, resulting in a high confidence level for the inferred function of the protein query sequence. The other types of hits can also shed light on the putative function of the query protein, with the confidence level of an individual hit indicated by its E value.
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The example above shows the search results, as of October 22, 2014, for protein GI 157830769 (Cyclodextrin Glucanotransferase). Hit types in the concise display can include specific hits, the superfamily to which the highest-ranking hit belongs, and multi-domain models. The CDD help document provides more information about: (1) display elements such as the colors/shapes used for the domain cartoons, the small triangles that represent conserved features/sites, the double-headed arrows that represent structural motifs; (2) display controls such as horizontal zoom and zoom to residue level; and (3) the options to search for similar domain architectures and refine search.
Click anywhere on the illustration to open the current, interactive CD-Search: Concise results page for protein GI 157830769. (Note: The live web page may look different from the illustration shown here, because the Conserved Domain Database continues to evolve with the addition of new data and the refinement of algorithms to identify specific hits and superfamilies. However, the concepts shown in the illustration remain stable.)
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