#!/usr/bin/env perl

use strict;
use warnings;

my %res;

{
    local $/ = "\n>";

    while (my $record = <DATA>) {
        chomp $record;
        $record = substr $record, 1 if $. == 1;
        $record =~ s/\s*\z//m;
        my ($id, $anno_seq) = split /\|/, $record, 2;
        push @{$res{$anno_seq}}, $id;
    }
}

print '>', join('|', (sort @{$res{$_}}), $_), "\n"
    for sort { $res{$a}[0] cmp $res{$b}[0] } keys %res;

__DATA__
>id7|anno2
GHI
>id1|anno1
ABC
>id6|anno1
ABC
>id4|anno2
GHI
>id2|anno3
DEF
>id3|anno1
ABC
>id5|anno1
ABC