From owner-biophysics@net.bio.net Fri Mar 25 22:00:00 1994 Newsgroups: bionet.molbio.proteins,bionet.biophysics Path: biosci!agate!ihnp4.ucsd.edu!swrinde!emory!news-feed-2.peachnet.edu!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: Equivalent amino acids for similarity searches Message-ID: Organization: Frederick Cancer Research and Development Center References: <2mmfdp$t1n@usenet.INS.CWRU.Edu> Date: Sat, 26 Mar 1994 04:53:34 GMT Lines: 22 Xref: biosci bionet.molbio.proteins:1635 bionet.biophysics:145 3~ In article <2mmfdp$t1n@usenet.INS.CWRU.Edu> dy684@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 >function. 3~ 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@ncifcrf.gov .