ConSurfDB vs. ConSurf: Difference between revisions
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====APD 0.31==== | ====APD 0.31==== | ||
{{Template:ColorKey_ConSurf_NoYellow_NoGray}} | {{Template:ColorKey_ConSurf_NoYellow_NoGray}} | ||
By default, ConSurf Server excludes from the multiple sequence alignment sequences with >95% identity, or <35% identity with the query sequence. Changing those limits to >98% and <70% reduced the default APD of 1.1 to 0.31. This result shows high conservation of the following residues in the groove: | By default, ConSurf Server excludes from the multiple sequence alignment sequences with >95% identity, or <35% identity with the query sequence. Changing those limits to >98% and <70% reduced the default APD of 1.1 to 0.31. This result shows high conservation of the following residues in the groove: | ||
* <span style="background-color:#961d54;color:white;padding-left:0. | * <span style="background-color:#961d54;color:white;padding-left:0.4em;padding-right:0.4em;padding-top:0.2em;">Level 9:</span>. | ||
**Tyr7: hydrogen bonds to the main chain oxygen of peptide amino acid 1. | **Tyr7: hydrogen bonds to the main chain oxygen of peptide amino acid 1. | ||
**Lys146: salt bridges to the carboxy terminus of the peptide. | **Lys146: salt bridges to the carboxy terminus of the peptide. | ||
