Conservation, Evolutionary: Difference between revisions
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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 ConSurfDB] 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. | 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 ConSurfDB] 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 ConSurfDB] 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 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 ConSurfDB-colored sequence-different chains do not have exactly the same levels of conservation. | 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 ConSurfDB] 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 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 ConSurfDB-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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