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, not surprisingly, 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. | 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, not surprisingly, 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 sequence-different chains do not have exactly the same levels of conservation. | ||
Therefore, residues with, for example, conservation level 9 (maximal conservation) in each of the three sequence-different chains do not have exactly the same levels of conservation. | |||
<center> | |||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
! Chain | ! Chain | ||
! Length | |||
! Number of sequences in MSA | ! Number of sequences in MSA | ||
! APD | ! APD | ||
|- | |- | ||
| A | | A | ||
| 274 | |||
| 144 | | 144 | ||
| 1.72 | | 1.72 | ||
|- | |- | ||
| B | | B | ||
| 99 | |||
| 75 | | 75 | ||
| 1.49 | | 1.49 | ||
|- | |- | ||
| C | | C | ||
| colspan=" | | colspan="3" | Length below minimum for ConSurf | ||
|- | |- | ||
| G | | G | ||
| 129 | |||
| 201 | | 201 | ||
| 1.35 | | 1.35 | ||
|} | |} | ||
</center> | |||
In Proteopedia's ''Evolutionary Conservation'' scenes, we have chosen to color all the chains in the molecule at once. This gives a potentially useful overview, but can be misleading unless one realizes that a given conservation color, in two sequence-different chains, does not mean exactly the same level of conservation. In contrast to Proteopedia's ''Evolutionary Conservation'' scenes, ConSurfDB and ConSurf Server apply conservation level colors to only one chain sequence at a time, thereby avoiding this possible confusion. | In Proteopedia's ''Evolutionary Conservation'' scenes, we have chosen to color all the chains in the molecule at once. This gives a potentially useful overview, but can be misleading unless one realizes that a given conservation color, in two sequence-different chains, does not mean exactly the same level of conservation. In contrast to Proteopedia's ''Evolutionary Conservation'' scenes, ConSurfDB and ConSurf Server apply conservation level colors to only one chain sequence at a time, thereby avoiding this possible confusion. | ||
