[BiO BB] Finding (Predicting) a Proein family in a new organism using only Bioinformatics approach

[hamid]

Hi buddy,
I have a question regarding to find a new protein family in a new organism.
Suppose we have the whole proteome of organism "O", although we have 200 
proteins regarding to protein family "F" those belongs to several subunits 
of complete system "S".  We doubt whether there is system "S" in organism 
"O" or not. I have done a multiple alignment among whole proteome of "O" 
(almost 1200 proteins) and all the proteins belonging to "F" acheieved from 
several  organisms those are proven to have system "S" in them. I achieved a 
huge alignment file. Now I do not know how can I find that are there any 
proteins in "O" proteome relating to "F" family.
Please guide me in this regard.
Yours
Behnam
 
/*
Hamid( Behnam )Nikbakht,
M.Sc of Cell and Molecular Sciences
Bioinformatics Center
Laboratory of Biophysics and Molecular Biology
Institute of Biochemistry and Biophysics
University of Tehran
P.O.Box 13145-1384
Tehran, Iran.
Tel: (+98 21) 664-98672
Fax: (+98 21) 669-56985
Alt. E-Mail : hamid at ibb.ut.ac.ir
*/
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