ConSurfDB vs. ConSurf: Difference between revisions
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====ConSurf Server Default APD 1.1==== | ====ConSurf Server Default APD 1.1==== | ||
[[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>)<ref name="apd1.1">Default ConSurf Server settings: UniRef90 database, | [[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>)<ref name="apd1.1">Default ConSurf Server settings: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = β-2 microglobulin) and the 8 amino acid peptide (chain P) are shown as gray backbone traces. | ||
Conservation of important residues in the groove is obscured by inclusion in the MSA of proteins with different functions ([[#Example With Multiple Functions|see analysis above]]). The sides of the groove are variable due to many alleles that enable it to bind a wide range of peptide sequences. The only groove residue that is conserved at greater than level 7 is '''Tyr159''' (level 8), whose sidechain hydrogen bonds the main-chain oxygen of the amino-terminal peptide residue. Only a handful of surface residues are highly conserved (level 9), including '''Trp274''' involved in binding CD8. | Conservation of important residues in the groove is obscured by inclusion in the MSA of proteins with different functions ([[#Example With Multiple Functions|see analysis above]]). The sides of the groove are variable due to many alleles that enable it to bind a wide range of peptide sequences. The only groove residue that is conserved at greater than level 7 is '''Tyr159''' (level 8), whose sidechain hydrogen bonds the main-chain oxygen of the amino-terminal peptide residue. Only a handful of surface residues are highly conserved (level 9), including '''Trp274''' involved in binding CD8. | ||
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{{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 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>. This result reveals high conservation of the following key residues in the groove: | ||
* <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. | ||
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(Tyr159 was level 6.) | (Tyr159 was level 6.) | ||
Another custom ConSurf Server job gave an APD of 0.30, but levels for the above 4 groove residues were 7-8. These lower levels can be accounted for by the highest expectation value in the MSA, which was 10 to the power ―141. In contrast, for the job with APD 0.31, the highest expectation value was 10 to the power ―84. | Another custom ConSurf Server job<ref name="apd0.30">Custom ConSurf Server settings for APD 0.30: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has '''250''' sequences '''closest''' to the query.</ref> gave an APD of 0.30, but levels for the above 4 groove residues were 7-8. These lower levels can be accounted for by the highest expectation value in the MSA, which was 10 to the power ―141. In contrast, for the job with APD 0.31, the highest expectation value was 10 to the power ―84. | ||
<font color="red">UPDATE IN PROGRESS:</FONT> [[User:Eric Martz|Eric Martz]] 15:02, 29 July 2024 (UTC) | <font color="red">UPDATE IN PROGRESS:</FONT> [[User:Eric Martz|Eric Martz]] 15:02, 29 July 2024 (UTC) | ||
