#!/usr/bin/env perl

use 5.014;
use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        my ($top, $seq) = split /\n/, $_, 2;
        print '>' unless $. == 1;
        say $top;
        say $seq =~ y/\n//dr;
    }
}

__DATA__
> gi|11SB_CUCMA Train|1 21
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGS
EVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAPKLIFV
AQGFGIRGIAIPGCAETYQT
SSSSSSSSSSSSSSSSSSSSS....................
...........................
.................
..........
> gi|1A43_HUMAN Train|1 24
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPG
RGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWSQTDRANLGTLRGYYNQSEDGSHTIQR
MYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKWETAHEAE
SSSSSSSSSSSSSSSSSSSSSSSS.........................................................................................
.............
..........................................