Equivalent amino acids for similarity searches

Joe Mack mack at ncifcrf.gov
Fri Mar 25 23:53:34 EST 1994

In article <2mmfdp$t1n at usenet.INS.CWRU.Edu> dy684 at cleveland.Freenet.Edu (Roberto Albinoni) writes:
>i am comparing the dna-derived amino acids sequences of two proteins in
>order to determine which residues may be most important to enzymatic
To do this you need a large number of proteins in the family , large enough 
and divergent enough that you have a good sampling of sequence space. In this
you know that a residue that is conserved in your list of proteins is actually
conserved in the family and not an artifact of limited sampling. This can't be
done with two proteins usually. If you have one enzyme from E.coli and one from
elephants, and you only have a small number of identical residues, then you can
be reasonably confident that they are required for activity. 

	Residues involved in catalysis are IDENTICAL throughout the family. 
Since identical structures can be made from many different residues, identical
structural motifes do not need identical residues to produce them.

	Joe Mack
	mack at ncifcrf.gov

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