• 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. 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.


• The small triangles beneath the query protein on a CD-Search results page indicate the residues that comprise conserved features/sites, such as binding or catalytic sites, as mapped from the conserved domain annotations to the query sequence. The triangles are shown in the same color as the domain on which they have been annotated and appear if a region of the query protein sequence: (1) gets a specific hit to a domain model on which conserved features/sites have been annotated, OR (2) gets a non-specific hit to a domain model that belongs to a superfamily whose representative is an NCBI-curated domain that has such annotations. (These hit types are shown on illustrations of the CD-Search results Concise Display and Full Display.)


• Click on the triangles to view details about the feature, including a multiple sequence alignment of your query sequence and the protein sequences used to curate the domain model. Hash marks (#) above the aligned sequences show the location of the conserved feature residues (see illustration in help document). A thumbnail image, if present, provides an approximate view of the feature's location in three dimensions and options for interactive 3D structure viewing.