Update 2: As revealed in the crosspost linked here, the true format of the OPed example file seems to be standard FASTA, so the correct approach is along the lines used by choroba here.

---

Is this the correct way of doing it?

No.

You should always have the statements
    use strict;
    use warnings;
at the start of your code (see strict and warnings). If you place these statements at the beginning of the OPed code, what happens? Some questions:

• In the  while (my $line=<FILE1>) { ... } loop, what is the scope of the  $line variable?
• In the  if ($line =~ /CDECGKEFSQGAHLQTHQKVH/) { ... } conditional, where was  $line ever defined/declared? Is this expression valid under strict?

Please see Basic debugging checklist.

Maybe try something like:

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";
        }

    }
[download]

Note: This has not been tested with multiple FASTA records, only with the single record example given in the OP.

Update 1: (Update: Nevermind. See Update 2 above.) I have a slightly simpler version of this script that I've tested (minimally) with a two-record FASTA file. Please let me know if you're interested.

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