Welcome to the forum @microuser2 !
QIIME 2 uses ANY database that you feed it 
It is by no means restricted to Greengenes — we provide pre-trained classifiers for Greengenes and SILVA on our website, but other commonly used databases that are compatible more or less "off the shelf" include GTDB, UNITE, and any other database that uses compatible file formats (FASTA and tab-delimited taxonomy files)
We even have a tutorial for using RESCRIPt (an external plugin) to compile a QIIME 2-formatted database from NCBI Genbank (this example uses the 16S RefSeqs):
https://forum.qiime2.org/t/using-rescript-to-compile-sequence-databases-and-taxonomy-classifiers-from-ncbi-genbank/15947/10
But it sounds like you have already processed data that was classified (or clustered) using Greengenes, and now want to map to NCBI sequences... you could use q2-feature-classifier to perform this mapping, e.g., to BLAST to find the top hit. Alternatively, just copy and paste the sequence that you want into NCBI BLAST to find the closest match...
Good luck!