use strict;
use warnings;

my $i = 1;

while (<>) {
	s/>\K.+/$i++/e;
	print;
}

##</code><code>##

>1

MNLTFDYTKEPSRDVLCIDVKSFYASVECVERG LDPLKTMLVVMSNSENSGGLVLAASPM

>2

MKQNRKEFSSYFSRSIKQNKPLYLLLMSSETNPF PRPVIGTFRGYVEENKIIIGEDSYSI