Perhaps you want something like this (UNTESTED):

use strict;
use warnings;


my $list_file = '/g/Viruses/prophage_data/emptySeqList_aa.txt';
my $ptt_file  = '/g/Viruses/prophage_data/prophage_region.ptt1';


## list of 83 to remove from ptt file
open my $IN, '<', $list_file or die "Cannot open '$list_file' because:
+ $!";

my %empty_geneids;
while ( <$IN> ) {
    my ( $header ) = split;
    if ( /^>([^_]+_[^_]+)/ ) {
        $empty_geneids{ $1 } = 1;
        print "empty gene_id from list file\t$1\n";
        }
    }
close $IN;

my $empty_geneids_pattern = join '|', keys %empty_geneids;


open my $PTT, '<', $ptt_file or die "Cannot open '$ptt_file' because: 
+$!";
open my $OUT, '>', "$ptt_file.noEmpties" or die "Cannot open '$ptt_fil
+e.noEmpties' because: $!";


while ( <$PTT> ) {
    next if /$empty_geneids_pattern/;
    print $OUT $_;
    }
close $OUT;
close $PTT;
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