#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11144847
use warnings;

my %res;
/(id\d+)(.*)/s and push @{ $res{$2} }, $1 for split />/, join '', <DATA>;
for ( sort keys %res )
  {
  local $" = '|';
  print ">@{$res{$_}}$_";
  }

__DATA__
>id1|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id2|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id3|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id4|Q51487|P-474-4|86-98,113-126,297-310,322-335 alt
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id5|Q51487|P-474-4|86-98,113-126,297-310,322-335 alt
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE