if it's an option to slurp the file before processing, like:

...
my $fn = 'data.dat';
my $stuff;
open my$fh, '<', 'data.dat' or die "$fn - $!";
{ local $/; $stuff = <$fh> }
close $fh;
...
[download]

then the program could be simplified like:

...
while( $stuff =~ /^ (\d+): \s+            # the number xx: => $1
                    (\w+)  \s+            # the locus => $2
                    ( (?:.(?!^\d+:))+ )   # the remaining record => $3
                 /msgx ) {
   my ($locus, $name, $record, $kegg, $func, $proc, $comp) = ($2, '', 
+$3, ('unknown')x4);
   $name = $1 if $record =~ /([^\n\[]+)\s*/;
   $kegg = $1 if $record =~ /KEGG \s+ pathway: \s+ (.+?)\s+Function \s
++ Evidence/sx;
   $func = $1 if $record =~ /Function  \s+ Evidence \s+ (.+?) (?:\n\n|
+\z)/sx;
   $proc = $1 if $record =~ /Process   \s+ Evidence \s+ (.+?) (?:\n\n|
+\z)/sx;
   $comp = $1 if $record =~ /Component \s+ Evidence \s+ (.+?) (?:\n\n|
+\z)/sx;
   print join "\n\n", $locus, $name, $kegg, $func, $proc, $comp;
}
...
[download]

Regards

mwa