#!/usr/bin/perl -l
use warnings;
use strict;

use Inline::Files;

my %file1;

while (<FILE1>) {
    next if /^\s+$/;
    my ( $key, $value ) = split;
    $file1{$key} = $value;
}
my $str_union;
my $str_inter;

while (<FILE2>) {
    next if /^\s+$/;
    my ( $key, $value ) = split;
    if ( $file1{$key} ) {
        $str_union .= $_;
    }
    else {
        $str_inter .= $_;
    }
}

print "This goes to File 3\n", $str_union,
  "\nThis goes to File 4\n", $str_inter;

__FILE1__
EC:1.1.1.42    isocitratedehydrogenase
EC:1.1.1.44    6-phosphogluconatedehydrogenase
EC:1.1.1.49    glucose-6-phosphate1-dehydrogenase

__FILE2__
EC:1.1.1.42    isocitratedehydrogenase
EC:1.1.1.44    6-phosphogluconatedehydrogenase
EC:1.1.1.49    glucose-6-phosphate1-dehydrogenase

EC:1.11.1.9    glutathioneperoxidase
EC:2.5.1.16    spermidinesynthase

EC:6.3.1.8    glutathionesynthase