The Phmmer search tool searches for query sequence matches in sequence database, much as BLASTP or FASTA would do.
The Phmmer search works essentially like the HMM3 search does, except you provide a query sequence instead of a query profile HMM.
The database sequence must be selected in the Project View or there must be an active Sequence View window opened.
Select the query sequence in the Phmmer search dialog:
You can set options of the Phmmer search by choosing the needed dialog tab. Here you can see the e-value calibration options:
The results are stored as sequence annotations in the Genbank file format.