Fig. 3

The hits’ page displays schematic and detailed alignments of the structural hits identified with the input protein (or the proteins) spanning the input genomic coordinates. a Schematic display of the alignment and the spanned regions. Horizontal colored bars, presented in a manner similar to Blast’s results page, serve as links to the detailed alignments located later in the page. The green bar indicates the query protein; red bars indicate PDB hits; while blue bars indicate ModBase models of the query proteins. Several isoforms might be found for the input protein. b Detailed alignments of the query protein (upper sequence line) and structure hits. Two sequence lines appear for the structure hit. One shows the protein sequence (PDB SEQRES record) and the second shows the sequence of the resolved coordinates (PDB ATOM record). In the first two alignments in this example (Q61 in NRAS) the loop which contains the variant is missing while in the third it is present. Description of the structure hits and indications for the alignment quality precede the alignment display. Residues which appear in dbSNP, Cosmic and Clinvar databases are indicated by various colors on the query sequence. The input variant is indicated by green arrows below and above the alignments. A link to the JSmol structure visualization page follows the alignment