ConSurfDB vs. ConSurf: Difference between revisions
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<span style="float:right;">{{Template:ColorKey_ConSurf_NoYellow_NoGray}}</span> | <span style="float:right;">{{Template:ColorKey_ConSurf_NoYellow_NoGray}}</span> | ||
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<ref name="apd0.31">Custom ConSurf Server settings for APD 0.31: UniRef90 database, excluding sequences with '''> 98% or < 70%''' identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref>. This result reveals high conservation of the following key 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<ref name="apd0.31">Custom ConSurf Server settings for APD 0.31: UniRef90 database, excluding sequences with '''> 98% or < 70%''' identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref>. <scene name='39/399854/2vaa_apd_point31/1'>This result reveals high conservation of the following key residues in the groove</scene>: | ||
* <span style="background-color:#961d54;color:white;padding:0.2em 0.4em 0.1em 0.4em;">Level 9:</span> | * <span style="background-color:#961d54;color:white;padding:0.2em 0.4em 0.1em 0.4em;">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. | ||
