I am trying to run delta blast. However, I am being extremely confused how to do it properly. The stuff I understand right now:

1. First, I should download cdd_delta database from ncbi using update_blastdb.pl. Check.
2. Use makeprofiledb to convert cdd into a rpsblast compatible database. I have no clue how to do this. I've read that I should create scoremat (pssm, .smp) files and feed them into makeprofiledb, but I couldn't find any tutorials or articles on this. What are smp files and how can I create them from my database?
3. Use makeblastdb on my search database and then run deltablast.

Step 2 is where I am stumbling. If I have a list of proteins which I want to use as queries/subjects to my search, how can I convert them to smp files?

In short, if I have a set of proteins to use as queries, along with a database, both in fasta format, how to properly run deltablast on this? Thanks.