How To Use the Conserved Domain Database (CDD): identify putative protein function

• 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.

CD-Search results concise display (default), which shows only the top-scoring hits for each region of the query sequence (protein GI 157830769, Cyclodextrin Glucanotransferase). Click anywhere on the graphic to open the actual, interactive CD-Search results page.