Conservation, Evolutionary: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis, Wayne Decatur

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 This caveat applies only to molecules that contain chains with different sequences. The conservation colors shown in Proteopedia's ''Evolutionary Conservation'' scenes do not indicate the same levels of conservation for chains of different sequences. This is because  [http://consurfdb.tau.ac.il ConSurf-DB] calculates conservation levels independently for each sequence-different chain, and the levels are relative to the multiple sequence alignment constructed for each sequence-independent chain.
-For example, consider [[1bqh]], which contains 10 chains, representing two copies of a 5-chain molecule. Each molecule contains four sequence-different chains. A visit to [http://consurfdb.tau.ac.il ConSurf-DB] reveals, as expected, that a different number of sequences was utilized for the multiple sequence alignment (MSA) and conservation calculations for each of these sequence-different chains, and that each MSA had a different [[ConSurfDB_vs._ConSurf#Average_Pairwise_Distance|average pairwise difference (APD)]], a measure of diversity within the MSA. Therefore, residues with, for example, conservation level 9 (maximal conservation) in each of the three ConSurf-DB-colored sequence-different chains have the highest levels of conservation within their own chain, but do not have exactly the same absolute levels of conservation.
+For example, consider [[1bqh]], which contains 5 chains with four distinct sequences. A visit to [http://consurfdb.tau.ac.il ConSurf-DB] reveals, as expected, that a different number of sequences was utilized for the multiple sequence alignment (MSA) and conservation calculations for each of these sequence-different chains, and that each MSA had a different [[ConSurfDB_vs._ConSurf#Average_Pairwise_Distance|average pairwise difference (APD)]], a measure of diversity within the MSA. Therefore, residues with, for example, conservation level 9 (maximal conservation) in each of the three ConSurf-DB-colored sequence-different chains have the highest levels of conservation within their own chain, but do not have exactly the same absolute levels of conservation.
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