I'm not 100% sure what you're trying to do with regards to your search in the first place, but I recommend using Sean Eddy's program [Jackhammer][1] it's similar to PSI-BLAST but uses Hammer HMM underpinnings.

As input it can take a single sequence, a multiple sequence alignment, or an existing HMM and then allow you to search in an iterative model building way.  You can also download an HMM too at any stage in the iterative search, as well as the results / alignment. 


  [1]: https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer