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=" | [[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="consurfdefault">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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====ConSurf Server Custom APD 0.51==== | ====ConSurf Server Custom APD 0.51==== | ||
A custom consurf job resulting in an APD of 0.51<ref name="apd0.51">Custom ConSurf Server settings for APD 0.51: UniRef90 database, excluding sequences with > 95% or '''< 50%''' identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> (NOT SHOWN) had '''NO groove residues with conservation levels > 6'''. Trp274 was level 9. | A custom consurf job resulting in an APD of 0.51<ref name="apd0.51">Custom ConSurf Server settings for APD 0.51 with 2vaa: UniRef90 database, excluding sequences with > 95% or '''< 50%''' identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> (NOT SHOWN) had '''NO groove residues with conservation levels > 6'''. Trp274 was level 9. | ||
====ConSurf Server Custom APD 0.31==== | ====ConSurf Server Custom APD 0.31==== | ||
<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 4 key residues in the groove</scene> ({{Yelspan|yellow halos}}). With spin OFF, touch a residue to identify it. | 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 with 2vaa: 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> ({{Yelspan|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> | ||
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<scene name='39/399854/2vaa_peptide_contacts/1'>Here are all the polar residues contacting the peptide</scene>. Use the '''POPUP BUTTON''' to see details! (This scene is easily obtained in [http://firstglance.jmol.org FirstGlance]: Tools tab, click Contacts, check Label Contacts, and [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|made into a Green Link]].) | <scene name='39/399854/2vaa_peptide_contacts/1'>Here are all the polar residues contacting the peptide</scene>. Use the '''POPUP BUTTON''' to see details! (This scene is easily obtained in [http://firstglance.jmol.org FirstGlance]: Tools tab, click Contacts, check Label Contacts, and [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|made into a Green Link]].) | ||
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 with 2vaa: 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. | ||
===Case #2: UV Resistance Protein=== | ===Case #2: UV Resistance Protein=== | ||
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</tr><tr> | </tr><tr> | ||
<td> | <td> | ||
1.42<ref name=" | 1.42<ref name="consurfdefaults" /> | ||
</td><td> | </td><td> | ||
14% | 14% | ||
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</tr><tr> | </tr><tr> | ||
<td> | <td> | ||
0.91 | 0.91<ref name="apd0.91">ConSurf settings for APD 0.91 with 4dnw: Clean UniProt, 35-95%, 200 sequences closest to query.</ref> | ||
</td><td> | </td><td> | ||
16% | 16% | ||
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</tr><tr> | </tr><tr> | ||
<td> | <td> | ||
0.48 | 0.48<ref name="apd0.48">ConSurf settings for APD 0.48 with 4dnw: Clean UniProt, 35-95%, 125 sequences closest to query.</ref> | ||
</td><td> | </td><td> | ||
18% | 18% | ||
