Your question is not clear. What exactly are you trying to get? All the orthologous proteins from multiple species for a query bacterial proteome of interest? Or some kind of orthologue grouping for all proteins in all proteomes?

If the former, I have a program to do that, GOPHER (http://rest.slimsuite.unsw.edu.au/gopher), part of SLiMSuite (https://github.com/slimsuite/SLiMSuite). It will need to re-run the BLAST searches as it goes. To get protein families that include paralogues, you can run HAQESAC (http://rest.slimsuite.unsw.edu.au/haqesac), which can be run on a proteome using MultiHAQ. What is your planned usage of these orthologue sets? Both these programs will generate alignments and trees, if that is what you ultimately need.

If what you need is to find two-way best hit from blast result tables, There are some tools in github (ie. https://github.com/Adamtaranto/blast-besties) . Or you can write a perl-script or python script manually to found the answer.

However, if you want to get gene family information from blast result, I think Richard's answer is what you are looking for. Multiple sequencing alignment and distance estimation would be a core part for that situation.

Best wishes.

What I understand from your question is pulling out all orthologous proteins of the 100 strains. Reciprocal Best Hit BLAST is your friend. You can find many scripts or write your proper one as suggested above. Another alternative is to use Galaxy server or create your instance.

try using orthofinder (https://github.com/davidemms/OrthoFinder). it does everything for you

You may also refer OrthoDB 9.1 (https://www.orthodb.org/) for unique ortholog genes.