I installed BLAST and CLUSTALW.
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I downloaded the protein and genome files for all the Bacteria.
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Using an awk script, I filtered out all the proteins lacking an
upstream region of at least 50 base pairs.
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Using the filtered proteins, I created a BLAST database to query against.
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I took the filtered protein list for Streptococcus pyogenes, and ran
it against the new BLAST database.
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I processed the results using an awk script, gathering together all
the proteins and upstream segments into files for later processing.
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 I took 3 of the top hits (on the order of 500 matches), and ran
CLUSTALW on them.