#! /usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

my $seq;
while (<DATA>) {
    if (my $line_number = (/^>JJ22$/ ... /^>/)) {
        chomp;
        $seq .= $_ unless $line_number == 1 || $line_number =~ /E0/;
    }
}
my $count = () = $seq =~ /[MT].[KA]/g;
say $count;

__DATA__
>JJ57
MKIKLVTVGDAKEEYLIQGINEYLKRLNSYAKRETIEVPDEKAPEKLSDAEMLQVKEKEGEYVFVLAI
NGKQLSSEEFSKEIFQTGISGKSNLTFTTCFSLGLSDSVLQRIMKGEPYHKL
>JJ22
MDQNGASGSHPNRASTRKGAHARERGATVSAMSANRSNIIDEMAKICEADRQTFAIARRTRNESQ
FFGFRTASNKAIEITEAMEKRGAMFLTQSKATDQLNGWQPSDEPDKTSAESEPWFRGKQLSSEEFS
KEIFQTGISGKSNLTFTTCFSLGLSDSVLQRIMKGEPYHKL
>JJ41
MWKTVAPIFAAIFAVGLCGTFRTNTRKGEPTTKCFVFVHDTKARIYQCTFKTWSCPWLNNIVSAQF
QFVTGANYKIVVKLVGELFTETALFNWSSPTTIFTGLGTLITADKTLDCDSNML