Conservation, Evolutionary: Difference between revisions
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| The nine conservation grade colors utilized by ConSurf-DB and ConSurf, plus yellow for amino acids with insufficient data, and gray for chains that ConSurf could not process. See [[Help:Color Keys]]. | | The nine conservation grade colors utilized by ConSurf-DB and ConSurf, plus yellow for amino acids with insufficient data, and gray for chains that ConSurf could not process. See [[Help:Color Keys]]. | ||
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| colspan="2" |<br><ul><li>'''''Insufficient Data''''' describes amino acids for which a meaningful conservation level could not be derived from the set of homologous sequences utilized. This occurs when the confidence interval for the calculated conservation level is too large. For more, see the [[ConSurfDB_vs._ConSurf#ConSurf-DB_Process]]. | | colspan="2" |<br><ul><li>'''''Insufficient Data''''' describes amino acids for which a meaningful conservation level could not be derived from the set of homologous sequences utilized. This occurs when the confidence interval for the calculated conservation level is too large. For more, see the [[ConSurfDB_vs._ConSurf#ConSurf-DB_Process|ConSurfDB Process]]. | ||
For an example, show ''Evolutionary Conservation'' at [[1hgf]]. | For an example, show ''Evolutionary Conservation'' at [[1hgf]]. | ||
</li> | </li> | ||
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<li>'''''No Data''''' describes entire protein chains that could not be processed by ConSurf-DB. For details, see [[ConSurfDB_vs._ConSurf#ConSurf-DB_Process]]. | <li>'''''No Data''''' describes entire protein chains that could not be processed by ConSurf-DB. For details, see [[ConSurfDB_vs._ConSurf#ConSurf-DB_Process|ConSurfDB Process]]. | ||
For an example, show ''Evolutionary Conservation'' at [[1hgf]]. | For an example, show ''Evolutionary Conservation'' at [[1hgf]]. | ||
</li> | </li> | ||
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==Locating Conserved Patches== | ==Locating Conserved Patches== | ||
Patches of highly conserved amino acid residues on the surface of a protein molecular structure are good candidates for [[Site | functional sites]]. Nearly every article in Proteopedia that is '''titled with a [[PDB code]]''' has an ''Evolutionary Conservation'' section below the molecular scene. (Results could not be obtained for a small | Patches of highly conserved amino acid residues on the surface of a protein molecular structure are good candidates for [[Site | functional sites]]. Nearly every article in Proteopedia that is '''titled with a [[PDB code]]''' has an ''Evolutionary Conservation'' section below the molecular scene. (Results could not be obtained for a small | ||
percentage -- see [[ConSurfDB_vs._ConSurf#ConSurf-DB_Process]].) Clicking '''show''' in the blue ''Evolutionary Conservation'' bar automatically colors all chains in the molecule by evolutionary conservation as calculated by ConSurf-DB. | percentage -- see [[ConSurfDB_vs._ConSurf#ConSurf-DB_Process|ConSurfDB Process]].) Clicking '''show''' in the blue ''Evolutionary Conservation'' bar automatically colors all chains in the molecule by evolutionary conservation as calculated by ConSurf-DB. | ||
Briefly, ConSurf-DB gathers sequences similar to that of the protein in question, then constructs a multiple sequence alignment, and analyses it for sequence positions that are conserved (have lower than average differences between sequences) and that are variable (have higher than average differences between sequences). Each amino acid is assigned a conservation score and corresponding color in Proteopedia's interactive 3D molecular scene. | Briefly, ConSurf-DB gathers sequences similar to that of the protein in question, then constructs a multiple sequence alignment, and analyses it for sequence positions that are conserved (have lower than average differences between sequences) and that are variable (have higher than average differences between sequences). Each amino acid is assigned a conservation score and corresponding color in Proteopedia's interactive 3D molecular scene. | ||
