ConSurfDB vs. ConSurf: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 143: | Line 143: | ||
<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>. <scene name='39/399854/2vaa_apd_point31/3'>This result reveals high conservation of the following key residues in the groove</scene>. | 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_point31/3'>This result reveals high conservation of the following 4 key residues in the groove</scene> (yellow halos). With spin OFF, touch a residue to identify it. | ||
* <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 amino terminus of the peptide. | **Tyr7: hydrogen bonds to the amino terminus of the peptide. (Floor of the groove, hard to see.) | ||
**Lys146: salt bridges to the carboxy terminus of the peptide. | **Lys146: salt bridges to the carboxy terminus of the peptide. | ||
* <span style="background-color:#ec6d96;color:white;padding:0.2em 0.4em 0.1em 0.4em;">Level 8:</span> | * <span style="background-color:#ec6d96;color:white;padding:0.2em 0.4em 0.1em 0.4em;">Level 8:</span> | ||
**Tyr84: hydrogen bonds to the peptide C-terminus. | **Tyr84: hydrogen bonds to the peptide C-terminus. | ||
**Thr143: hydrogen bonds to the peptide C-terminus. | **Thr143: hydrogen bonds to the peptide C-terminus. | ||
(Tyr159 was level 6.) | (Tyr159 was level 6. CD8 binding site Trp274 remains level 9.) | ||
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<ref name="evalue" /> 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<ref name="evalue" /> 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) | ||
