How to generate input MSA file

[CryoSky]

Hello,
I want to generate the input MSA file through hhblits. However, I found the output fasta file include lots of gaps like below:
-------------------------------------------------------------------------------------------------------------------------------------------------------T-----------------------------E----------------------R-----------------------Q-------------------------------I----------A-------H--I--------------------------IS-------------------T---M------------------------------------------------D---------------II---T------N------------------------------------------------H-T
Although my query sequence has only 137 residues, the output fasta file give me 3098 residues for each sequence if you load this file to GREMLIN. It's because hhblits aligned all founded sequence, I want to know do you have a code to align founded sequence to the first sequence (or your query sequence) in fasta?

[CryoSky]

Or could you share the command of hh-suite you use to prepare input files for GREMLIN? Many thanks!