You can use --noali and --tblout for the commandline options of nhmmer, to get a cleaner table.

Then you can extract the columns with name of the gene, and start and end of the sequence from the output table.

Here is an example:

awk '($1!~"#"){print "$4,$7,$8"}' file.out

You need to figure out which columns you need (col4,7,8 I put is just an example).

Then, if you have a file with all the gene sequences ($geneseqfile), with grep -A 1 $genename $geneseqfile you can grep the gene sequence, and use tail -n +2 | cut -c $start-$stop to get the subsequence.

Now, you can do this for all the hits using a while loop.

A simple while loop:

awk '($1!~"#"){print "$4,$7,$8"}' file.out | while read col1 col2 col3; do echo ">$col1" ;  grep -A $col1 $geneseqfile  | tail -n +2 | cut -c $col2-$col3 ; done