Save the output from perlblastparser into a file, which I will call test_data in the following.

The contents of test_data should look somewhat like this (note the empty line at the end of the file):

SW:X2:
     >SW:X2 A0KFJ6 Homoserine O-succinyltransferase GN=a PE=3 SV=1
     Length = 317
          e-118 201 0 299 Plus 1 299 1 299

SW:X3:
     >SW:X3 A0KFJ6 Homoserine O-succinyltransferase GN=b PE=3 SV=1
     Length = 317
          e-118 201 0 299 Plus

SW:X1:
     >SW:X1 A0KFJ6 Homoserine O-succinyltransferase GN=c PE=3 SV=1
     Length = 317
          e-118 201 0 299 Plus 1 299 1 299

Then create a Ruby script sortBy.rb like this:

lines = IO.readlines("test_data")

sortBy='GN='

entries = {}
n = 0

while n + 4 < lines.size do
        key = lines[n + 1].match(sortBy + '[^ ]+')[0].sub(sortBy, '')

        entries[key] = lines[n] + lines[n + 1] + lines[n + 2] + lines[n + 3] + lines[n + 4]

        n += 5
end

entries.keys.sort.each { |key|
        puts entries[key]
}

You can then sort your output by running: ruby sortBy.rb. Simply change the variable sortBy if you want to sort on something else than the GN field.