Not very elegant, but it seems to grab what you want: 
use strict;
use warnings;

while (<>) {
    if (/^DE|^GN|^ID/) {
        my $lines = $_;
        if ($lines =~ /^DE|^GN/ && $lines !~ /Putative uncharacterized
+ protein/)    {
            my @pairs = $lines =~ /(.+?=.+?;)/g;
            for my $pair (@pairs) {
                if ($pair =~ /=(.+);/) {
                    print lc($1), "\n";
                }
            }
        } elsif    ($lines =~ /^ID/)    {
            print " \n";
        }
    }
}

__END__

adp-ribosylation factor 1
arf1
arf, plarf

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In reply to Re: how to parse a UniProt Flat file by toolic
in thread how to parse a UniProt Flat file by stanleysj

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