DB_PREFIX is defined in your configure.php files.

If it's defined as blank, then Zen Cart assumes there is no prefix added to table names.
If it's defined as some value, then Zen Cart adds that prefix to the start of all table names when it generates a query to extract data from the database.

So, in the case of the "configuration" table, if the prefix is left blank, then Zen Cart looks for a table named "configuration". If the prefix is defined as "storedata_" then Zen Cart looks for a table named "storedata_configuration".

That's why the FAQ about moving hosts tells you to make sure you use the same DB_PREFIX setting in your new site as you did in your old site. That way when you import your data from the old server to the new one, your new store will be able to find the tables used for Zen Cart.