It's easy to set the maximum E-value threshold in a BLAST request. I need to set the minimum E-value. Does anybody have any suggestions?
Setting a minimum E-value threshold will result in literally every single entry in the database with E-values above that value, as they will have very large E-values. You will expect a million hits with 1000000 E-value, and as a result you will not get any useful information from the search.
Can you explain why you want to set a minimum E-value?
A suggestion to get less hits is to take another database, for proteins you could use the PDB database and get orders of magnitude less hits.
Thinking a little bit more about your question: Blasting is probably not the right approach for whatever you want to do. Even if you manage to set a minimum e-value, you'll probably still get huge clusters of similar proteins around that value, and I guess that's what you're trying to avoid.
Blasting is really good to find similar proteins, if you want to get a cross-section of whatever-ases, you need to dig into bioinformatics a lot more.