#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11152595
use warnings;

my $input = <<END;
>4kt0_M|P72986
MALSDTQILAALVVALLPAFLAFRLSTELYK
iiiiiiiiiMMMMMMMMMMMMMMMMMIIIII
>6uzv_m|P72986
MALSDTQILAALVVALLPAFLAFRLSTELYK
iiiiiiiiiiiiMMMMMMMMMMMMMMMMMII
>5oy0_m|P72986
MALSDTQILAALVVALLPAFLAFRLSTELYK
iiiiiiiiiMMMMMMMMMMMMMMMMMIIIII
>5oy0_m|P72986
MALSDTQILDIFFERENTAFLAFRLSTELYK
iiiiiiiiiMMMMMMMMMMMMMMMMMIIIII
>7oy0_m|P72996
MALSDTQILAALVVALLPAFLAFRLSTELYK
iiiiiiiiiMMMMMMMMMMMMMMMMMIIIII
>6hqb_M|P72986
MALSDTQILAALVVALLPAFLAFRLSTELYK
iiiiiiiiiiiMMMMMMMMMMMMMMIIIIII
END

my %unique;
for ( split /(?=>)/, $input )
  {
  $unique{ join "\n", (split /[|\n]/)[1, 2]} //= $_;
  }

use Data::Dump 'dd'; dd sort values %unique;