I would agree with sschneid.
You can't do what you are trying to do with a single ALTER TABLE command
You need to execute this SQL (through DBI or sqlplus):

CREATE SEQUENCE seq_the_table;
ALTER TABLE the_table ADD( the_table_seq NUMBER );
update the_table set the_table_seq = seq_the_table.NEXTVAL;
ALTER TABLE the_table ADD( PRIMARY KEY (the_table_seq));
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Hope that helps:)

Update
As far as the default seq_the_table.nextval goes.
Apparently you cannot use a sequence in the default clause.
At least in Oracle. You could use a before insert trigger
to set the_table_seq.