I am confused on how to do this step as it is has not worked for me so far.
What exactly did you try? Has it not worked because of incorrect blast installation, or you don't know how to formulate the command? If the latter, try this:
blastall -p blastp -i seq.fas -d seq.fas -m8 -o seq.cblast -e 1e-5
This assumes that you have all your sequences in
seq.fas and that you want to search them vs the same database. First you must format them with
formatdb command or use a different database with
-d. Once you have the output in
seq.cblast, you can follow this protocol.