use strict;
use warnings;

use Data::Dumper;

open my $inFH, q{<}, \ <<'END_OF_FILE' or die qq{open: $!\n};
>1gmz_B mol:protein length:122  PHOSPHOLIPASE A2
          Length = 122

 Score =  103 bits (233), Expect = 9e-23
 Identities = 56/124 (45%), Positives = 67/124 (54%), Gaps = 12/124 (9
+%)

Query: 2   LWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDS
+C 61
           LWQF  MI  K     P   +  YGCYCG+GG G P D  DRCC  HD CY    KL S
+C
Sbjct: 2   LWQFGKMI-LKETGKLPFPYYVTYGCYCGVGGRGGPKDATDRCCFVHDCCY---GKLTS
+C 57

Query: 62  KVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSK--VPYNKEHKNL
+D 119
           K     P T+ YSYS  +  I C  EN+ C   IC CD+ AA+CF +    YNK++ + 
+ 
Sbjct: 58  K-----PKTDRYSYSRKDGTIVC-GENDPCRKEICECDKAAAVCFRENLDTYNKKYMSY
+L 111

Query: 120 KKNC 123
           K  C
Sbjct: 112 KSLC 115

>1b4w_A mol:protein length:122  PROTEIN (PHOSPHOLIPASE A2)
          Length = 122

 Score = 95.7 bits (215), Expect = 2e-20
 Identities = 46/105 (43%), Positives = 61/105 (58%), Gaps = 10/105 (9
+%)

Query: 2   LWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDS
+C 61
           L QF  MIK K+   EP++ +  YGCYCG GG G P D  DRCC  HD CY   +K+  
+C
Sbjct: 2   LLQFRKMIK-KMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCY---EKVTG
+C 57

Query: 62  KVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICF 106
                +P  ++Y+YS  N  I C  + + C+  +C CD+ AAICF
Sbjct: 58  -----DPKWDDYTYSWKNGTIVCGGD-DPCKKEVCECDKAAAICF 96

END_OF_FILE

my $inHeader;
my $pushTo;
my @headers = ();
my @lines   = ();

while ( <$inFH> )
{
    chomp;
    if ( not $inHeader and m{^>} )
    {
        $inHeader = 1;
        $pushTo = \ @headers;
    }
    if ( $inHeader and m{^Query:} )
    {
        $inHeader = 0;
        $pushTo = \ @lines;
    }
    push @$pushTo, $_;
}

close $inFH or die qq{close: $!\n};

print Data::Dumper->Dumpxs(
   [ \ @headers, \ @lines ],
   [ qw{ *headers *lines } ],
   );
[download]

Here's the output.

@headers = (
             '>1gmz_B mol:protein length:122  PHOSPHOLIPASE A2',
             '          Length = 122',
             '',
             ' Score =  103 bits (233), Expect = 9e-23',
             ' Identities = 56/124 (45%), Positives = 67/124 (54%), Ga
+ps = 12/124 (9%)',
             '',
             '>1b4w_A mol:protein length:122  PROTEIN (PHOSPHOLIPASE A
+2)',
             '          Length = 122',
             '',
             ' Score = 95.7 bits (215), Expect = 2e-20',
             ' Identities = 46/105 (43%), Positives = 61/105 (58%), Ga
+ps = 10/105 (9%)',
             ''
           );
@lines = (
           'Query: 2   LWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTH
+DNCYKQAKKLDSC 61',
           '           LWQF  MI  K     P   +  YGCYCG+GG G P D  DRCC  H
+D CY    KL SC',
           'Sbjct: 2   LWQFGKMI-LKETGKLPFPYYVTYGCYCGVGGRGGPKDATDRCCFVH
+DCCY---GKLTSC 57',
           '',
           'Query: 62  KVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSK
+--VPYNKEHKNLD 119',
           '           K     P T+ YSYS  +  I C  EN+ C   IC CD+ AA+CF +
+    YNK++ +  ',
           'Sbjct: 58  K-----PKTDRYSYSRKDGTIVC-GENDPCRKEICECDKAAAVCFRE
+NLDTYNKKYMSYL 111',
           '',
           'Query: 120 KKNC 123',
           '           K  C',
           'Sbjct: 112 KSLC 115',
           '',
           'Query: 2   LWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTH
+DNCYKQAKKLDSC 61',
           '           L QF  MIK K+   EP++ +  YGCYCG GG G P D  DRCC  H
+D CY   +K+  C',
           'Sbjct: 2   LLQFRKMIK-KMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVH
+DCCY---EKVTGC 57',
           '',
           'Query: 62  KVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICF 1
+06',
           '                +P  ++Y+YS  N  I C  + + C+  +C CD+ AAICF',
           'Sbjct: 58  -----DPKWDDYTYSWKNGTIVCGGD-DPCKKEVCECDKAAAICF 9
+6',
           ''
         );
[download]

Some good habits to get into

• Always put use strict; and use warnings at the top of your scripts.

• Always test for success when open'ing and close'ing files.

• Avoid using scalars $a and $b as they are special and reserved for use with sort.

• Indent your code in a meaningful way to make the logic clearer and use it consistently.

• Use meaningful variable names (without making the names too long).

Cheers,

JohnGG

Update: The array ref. is not necessary as you can use a ternary to determine which array to push onto.

    push @{ $inHeader ? @headers : @lines }, $_;
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