[modeller_usage] Sequence consensus

[Cassiano <carromeu AT usp.br>]

Hi everybody!

I have a question about sequence alignment (i known that it isn't the 
subject of this forum, but i'll be very glad for any help). From a 
alignment, i intend to extract the consensus sequence differently. I 
keep only the aa that are really conserved (and probably structurally 
important). The others, I substituted by the aa G (for example: 
GGGDGGGRKGGGHEGG, where the aa D,R,K,H and E are very conserved in the 
protein's alignment). My aim is to modeler the consensus folding to the 
classes of protein in my study, emphasizing only the functionally 
important aa. I don't known if I really have a useful structural 
information or not. If not, i'll be very glad for any advice.

Thanks,
Cassiano Carromeu.