Can I look at functional assignments only for selected taxa or taxa responsible only for selected functions?

You can, but you will have to generate a new RMA-file for the subset of taxa/functions first.

First, select all the nodes of the taxonomy/ functional classification that you want to look at in detail.
Then select File -> Extract to New Document. (This option is only available for files saved in RMA6 format.)

If you selected functions, the new file will only be based on reads assigned with those functions and you can now see, what taxonomic assignment those reads have. Equally, if you selected a subset of taxa, you can now check which functional diversity these taxa provide.

How if I use DAA file for meganizer to perform annotation? Is there any alternative way to get functional assignments only for selected taxa?

At present extracting to a new document is the only way…

Thank you Dr. Daniel for your reply