But IIUC, the pattern to be searched for may be broken across multiple lines. How would your code handle, e.g., the record:

>AAF88103.1 zinc finger protein 226 [Homo sapiens]
AAAAAAAAAAAAAACDECGKEFSQ
GAHLQTHQKVHZZZZZZZZZZZ
[download]

Here's one way (snicker).
It shows the location of each occurrence, even if they are overlapping.

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11115501
use warnings;

$_ = do { local $/; <DATA> }; # or however you want to read the file

my $pattern = 'CDECGKEFSQGAHLQTHQKVH' =~ s/\B/\n?/gr;

print lc($`) . $1 . lc(substr $', length $1) . "\n" while /(?=($patter
+n))/g;

__DATA__
>AAF88103.1 zinc finger protein 226 [Homo sapiens]
MNMFKEAVTFKDVAVAFTEEELGLLGPAXRKLYRDVMVENFRNLLSVGHPPFKQDVSPIERNEQLWIMTT
ATRRQGNLGEKNQSKLITVQDRESEEELSCWQIWQQIANDLTRCQDSMINNSQCHKQGDFPYQVGTELSI
QISEDENYIVNKADGPNNTGNPEFPILRTQDSWRKTFLTESQRLNRDQQISIKNKLCQCKKGVDPIGWIS
HHDGHRVHKSEKSYRPNDYEKDNMKILTFDHNSMIHTGQKSYQCNECKKPFSDLSSFDLHQQLQSGEKSL
TCVERGKGFCYSPVLPVHQKVHVGEKLKCDECGKEFSQGAHLQTHQKVHVIEKPYKCKQCGKGFSRRSAL
NVHCKVHTAEKPYNCEECGRAFSQASHLQDHQRLHTGEKPFKCDACGKSFSRNSHLQSHQRVHTGEKPYK
CEECGKGFICSSNLYIHQRVHTGEKPYKCEECGKGFSRPSSLQAHQGVHTGEKSYICTVCGKGFTLSSNL
QAHQRVHTGEKPYKCNECGKSFRRNSHYQVHLVVHTGEKPYKCEICGKGFSQSSYLQIHQKAHSIEKPFK
CEECGQGFNQSSRLQIHQLIHTGEKPYKCEECGKGFSRRADLKIHCRIHTGEKPYNCEECGKVFRQASNL
LAHQRVHSGEKPFKCEECGKSFGRSAHLQAHQKVHTGDKPYKCDECGKGFKWSLNLDMHQRVHTGEKPYK
CGECGKYFSQASSLQLHQSVHTGEKPYKCDVCGKVFSRSSQLQSHQRVHTGEKPYKCEICGKSFSWRSNL
TVHHRIHVGDKSYKSNRGGKNIRESTQEKKSIK.
AAAAAAAAAAAAAACDECGKEFSQ
GAHLQTHQKVHZZZZZZZZZZZ
[download]

 

#!/usr/bin/perl -CSDA 

use utf8;
use Modern::Perl;
no warnings qw{uninitialized};
use Data::Dumper;
use Path::Tiny;

my $data = path('file,fasta')->slurp_utf8() =~ s/\s//mgr;
warn $data; 

print $data =~ /$_/  
        ? "The protein contains the domain -- $_\n"
        : "The protein doesn't contain the domain -- $_\n"
for 'KCKQCGKGFSRRSALNV', 'CGK', 'XXXX';

for my $lookfor (qw{CGK SQRLNR SQR PYKC PYKCK}) {
        pos $data = 0;
        while ($data =~ /$lookfor/gc) {
                print "there is $lookfor at ", (pos $data), "\n";
        }
}



result: 

AAF88103.1zincfingerprotein226[Homosapiens]MNMFKEAVTFKDVAVAFTEEELGLLGP
+AXRKLYRDVMVENFRNLLSVGHPPFKQDVSPIERNEQLWIMTTATRRQGNLGEKNQSKLITVQDRESEE
+ELSCWQIWQQIANDLTRCQDSMINNSQCHKQGDFPYQVGTELSIQISEDENYIVNKADGPNNTGNPEFP
+ILRTQDSWRKTFLTESQRLNRDQQISIKNKLCQCKKGVDPIGWISHHDGHRVHKSEKSYRPNDYEKDNM
+KILTFDHNSMIHTGQKSYQCNECKKPFSDLSSFDLHQQLQSGEKSLTCVERGKGFCYSPVLPVHQKVHV
+GEKLKCDECGKEFSQGAHLQTHQKVHVIEKPYKCKQCGKGFSRRSALNVHCKVHTAEKPYNCEECGRAF
+SQASHLQDHQRLHTGEKPFKCDACGKSFSRNSHLQSHQRVHTGEKPYKCEECGKGFICSSNLYIHQRVH
+TGEKPYKCEECGKGFSRPSSLQAHQGVHTGEKSYICTVCGKGFTLSSNLQAHQRVHTGEKPYKCNECGK
+SFRRNSHYQVHLVVHTGEKPYKCEICGKGFSQSSYLQIHQKAHSIEKPFKCEECGQGFNQSSRLQIHQL
+IHTGEKPYKCEECGKGFSRRADLKIHCRIHTGEKPYNCEECGKVFRQASNLLAHQRVHSGEKPFKCEEC
+GKSFGRSAHLQAHQKVHTGDKPYKCDECGKGFKWSLNLDMHQRVHTGEKPYKCGECGKYFSQASSLQLH
+QSVHTGEKPYKCDVCGKVFSRSSQLQSHQRVHTGEKPYKCEICGKSFSWRSNLTVHHRIHVGDKSYKSN
+RGGKNIRESTQEKKSIK at ./a.pl line 10.
The protein contains the domain -- KCKQCGKGFSRRSALNV
The protein contains the domain -- CGK
The protein doesn't contain the domain -- XXXX
there is CGK at 357
there is CGK at 385
there is CGK at 441
there is CGK at 469
there is CGK at 497
there is CGK at 525
there is CGK at 553
there is CGK at 581
there is CGK at 637
there is CGK at 665
there is CGK at 693
there is CGK at 721
there is CGK at 749
there is CGK at 777
there is CGK at 805
there is SQRLNR at 229
there is SQR at 226
there is PYKC at 380
there is PYKC at 464
there is PYKC at 492
there is PYKC at 548
there is PYKC at 576
there is PYKC at 632
there is PYKC at 716
there is PYKC at 744
there is PYKC at 772
there is PYKC at 800
there is PYKCK at 381
[download]

I think this is better than the previous suggestion. As for $lookfor though, this can be implemented more efficiently with the solution shown in Building Regex Alternations Dynamically.

By the way, I understand that perl -CSDA and use Modern::Perl; no warnings qw{uninitialized}; are likely your standard boilerplate, but typically code examples should be as self-contained as possible, i.e. not depend on modules that aren't necessary, and also no warnings in general isn't really a best practice. Although I personally sometimes get annoyed by uninitialized warnings myself, it's still not something I would recommend to a newcomer as it can hide problems.