In order to identify the sequences that are likely to be important for an enzyme's function I perform a BLAST search and then align the sequences of several orthologs which are 40%-99% similar. Then I go to PyMol, fetch the enzyme of interest, and manually color every amino acid that appears to have been highly conserved throughout the enzyme's evolution.
Is there a method to obtain the sequence similarity results in a format that can be easily transferred into PyMol? I would like to avoid the manual coloring step.
Once you have an alignment you can export the alignment score for each amino acid. This can then be inserted into the PDB file replacing the B value column. This can then be displayed in more sophisticated viewing software such as coot or ccp4i by colouring for Wilsons B-value. This should then display colours based on homology of your aligned proteins on the modelled proteins.
You could also think of using the ConSurf site.
http://consurftest.tau.ac.il/
It's open to everybody, quite easy to use, and the results can be readily displayed in PyMol. Basically, ConSurf can colour your given protein according to the conservation at every amino acid position. The conservation data can be supplied by the user in the form of a previously-generated multiple sequence alignment. Or, if you don't have an alignment handy, it can generate one for you. All-in-all, it's quite a handy tool to have at your disposal. Hope that helps.
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