while (my $seq = <$IN>) {  
   if ($seq =~ /^>(\w+).+\((\d+)\s+aa\)$/) {
      %sequence = (
           $1 => $2,
      );
      my $max = max(values %sequence);
         for (keys %sequence) {
            delete $sequence{$_} unless $sequence{$_} == $max
      }
      print Dumper(\%sequence);

      while ( my ($key, $value) = each(%sequence) ) {
        print $OUT "$key $value\n";
      }
   }
}

##</code><code>##

CIMG_00046 => 399
CIMG_00047 => 865
CIMG_00048 => 330
CIMG_00048 => 506
CIMG_00053 => 167
CIMG_00063 => 468

##</code><code>##

CIMG_00046 => 399
CIMG_00047 => 865
CIMG_00048 => 506
CIMG_00053 => 167
CIMG_00063 => 468