Hi Sangeetha,
Have a look at the following MSDN link showing the different platform and product versions supported with different suite of adapters from BizTalk:
http://www.microsoft.com/biztalk/en/us/adapters-included.aspx
As noted, AS400 V6R1 is NOT in the list of editions supported by BizTalk 2009 DB2 Adapter, so you are pretty much on your own on a trial-and-error basis if you upgrade DB2 to V6R1.
Daniel.