[BiO BB] help with bacterial protein sequence comparisons

[Phoebe Rice]

I need some hints from people who really know how to deal with the burgeoning database (I'm a crystallographer / biochemist):

I'm interested in the catalytic domain of a protein found on many plasmids & transposons.  I'd like to make a "sequence logo" or other informative-at-a-glance display of which residues are most conserved. 
Blast gives me pages of 99% identical proteins (mostly from other S. aureus strains), and I'm too lazy to pick "representatives" manually from further down the list.  What is the best way to get a list of related proteins that are all, say, <90% identical to other proteins in the list?

many thanks,
   Phoebe

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Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp