Conserved Domains and Protein Classification
How to view a protein query sequence embedded within the multiple sequence alignment of a domain model
  A Use the CD-Search tool to compare a protein query sequence (either as raw sequence data in FASTA format, or as a GI or Accession) against the desired conserved domain data set, in order to identify functional units within the query sequence. Or, simply retrieve a sequence record of interest from Entrez Protein database, open its "Links" menu, and select "Conserved Domains".  
  B 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.  
  C Click on a domain cartoon (colored bar representing a domain footprint) in the graphical display of the CD-search results to view the multiple sequence alignment for that domain model.  
  D Your query sequence will automatically be embedded in the alignment. If desired, modify the number and type of sequences shown as described in the help document section on CDD Record : multiple sequence alignment displays. It is also possible to view the query sequence embedded within a phylogenetic tree of the domain model's member sequences, if your hit was to an NCBI-curated domain.  

Illustration showing how to embed a protein query sequence in a conserved domain model multiple sequence alignment.

Revised 26 September 2016