Anser to https://www.biostars.org/p/9515563/

biostars_p_9515563.pl

#!/usr/bin/env perl
use strict;
use warnings;
my %h = ();
my $range = 5; # configures the maximum distance
keys(%h) = 72553; # pre-size hash to number of expected entries, should not be too large
  # read file into a hash first,
  # we don't trust the sorting order of the file,
  # if that uses too much memory, the file needed to
  # be sorted by species name and the code adapted
  <>; # skip header
while(<>){
  chomp;
  next if /^\s*$/; # skip empty
  my ($s,undef) = split;
  my ($prefix,$index) = split "_peg_", $s;
  die "invalid index $index" unless $index =~ /^\d+$/; # only digits
  push @{$h{"$prefix"}}, {index=>$index, line=>$_}
}
## check the specific condition for each gene and per species
foreach my $k (sort(keys(%h))){
  my $v = $h{$k};
  # compare all against all
  while (my $i = pop (@$v)) { # 1/2 of all comparisons 
    PAIR: foreach my $j (@$v) {     
      if  (abs($i->{'index'} - $j->{'index'}) <= $range) {
	print $i->{'line'},"\n",$j->{'line'},"\n";
      }
    }
  }
}

__END__

biostars_p_9515563_test.txt

Protein Ids domain


Abiotrophia_defectiva_peg_0144  wzz

Abiotrophia_defectiva_peg_0198  wxy

Abiotrophia_defectiva_peg_0200  wzz

Abiotrophia_defectiva_peg_0215  wca

Abyssicoccus_albus_peg_1185 wzz

Abyssicoccus_albus_peg_1189 wzx

Abyssicoccus_albus_peg_1200 wza

Abyssicoccus_albus_peg_1322 wca

Abyssicoccus_albus_peg_1324 wbb

Bradyrhizobium_elkanii_peg_6717 wac

Bradyrhizobium_elkanii_peg_6718 wzx

Bradyrhizobium_elkanii_peg_6721 waa

Bradyrhizobium_elkanii_peg_6752 wca

Bradyrhizobium_elkanii_peg_6780 wvx

Abyssicoccus_albus_123_peg_1185 wzz

Abyssicoccus_albus_123_peg_1189 wzx

Abyssicoccus_albus_123_peg_1200 wza

Abyssicoccus_albus_123_peg_1322 wca

Abyssicoccus_albus_123_peg_1324 wbb

usage:
perl biostars_p_9515563.pl biostars_p_9515563_test.txt