use strict;
use warnings;

use autodie;

use constant START_FASTA_REC => qr{ \A [^\]]+ \]  }xms;
use constant SUB_SEQUENCE    => qr{ CDECGKEFSQGAHLQTHQKVH }xms;
# use constant SUB_SEQUENCE  => qr{ NOT_PRESENT }xms;  # for debug

MAIN {

my $filename = 'file,fasta';
open my $fh_fasta, '<', $filename;

my $fasta_record;

LINE:
while (my $line = <$fh_fasta>) {

    chomp $line;

    if ($line =~ s{ ${ \START_FASTA_REC }}''xms) {
        process_fasta_record($fasta_record)
            if defined $fasta_record and length $fasta_record;
        $fasta_record = $line;
        next LINE;
        }

    $fasta_record .= $line;

    }

close $fh_fasta;

# process final fasta record.
process_fasta_record($fasta_record)
    if defined $fasta_record and length $fasta_record;

exit;  # normal exit from MAIN block

}  # end MAIN block

die "unexpected exit from MAIN block";

# subroutines ######################################################

sub process_fasta_record {

    my ($fasta_record,
        ) = @_;

    print "'$fasta_record' \n";  # for debug

    if ($fasta_record =~ SUB_SEQUENCE) {
        print "The protein contains the domain";
        }
    else {
        print "The protein doesn't contain the domain";
        }

    }