How to work with Uniprot-mapped data

I have several full metagenomes that have been run through BLAST to generate protein databases. They are all mapped to Uniprot Acc numbers.
Can I use this as input? -if so, how?

MEGAN needs to map uniprot Ids to taxon ids (and other ids, if you want to use e.g. the InterPro2GO viewer as well). You will need create a “synonyms file” for each classification that you want to use that says how to map words in your alignment reference header lines to taxon ids and other ids.
Producing those could be quite painful…

How about rerunning them using DIAMOND to compare against the NR database?