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search with gapped protein consensus-sequence from higher eukaryotes in yeast protein database

Schwarz Markus markus.schwarz at biologie.uni-regensburg.de
Mon Oct 22 07:35:25 EST 2001

Dear Sirs and Madams!
I would be very glad to get help from you for the following problem: I
want to search the protein-database from saccharomyces cerevisiae 
with no certain protein-sequence, but a gapped consensus-sequence for 
a conserved domain of a enzyme from higher eukaryotes to find a 
corresponding enzyme in yeast. This consensus-sequence is already 
based on very low sequence-identity: initially only detected by the 
STAMP-Program(Strucure based sequence alignment) because of 
preferentially conserved structure was later also a Psi-Blast search 
successful, based on the evolutionary most conserved protein found by 
the STAMP-search. 
With what program can the yeast database be searched for a gapped 
consensus-motive (established by a structure based sequence 
alignment)? Thank you very much
for your kind answer,
Markus Schwarz.


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