The next step then would be to compare what you have in $line to a hardcoded value. Like I already said, you most likely have a newline (and/or other stuff) at the end of $line and want to remove that before sending it off to the server:

while( defined( my $line=<FILE> )) {
    my $sequence= "ecNumber*$line#source*Swiss-Prot#textmining*0";
    print "Retrieving [$sequence]\n";
    $resultString = SOAP::Lite
    -> uri('http://www.brenda-enzymes.org/soap2')
    -> proxy('http://www.brenda-enzymes.org/soap2/brenda_server.php')
    -> getSequence($sequence)
    -> result;   
};
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