In that case you need to use -db 16sBLASTdb when you are doing the blast search.
That said, are you not using the latest Blast+ package where the command is now makeblastdb?
Code:
$ blastn -query unibac.fasta -db 16sBLASTdb -out blastn.outfmt6 -evalue 1e-5 -num_threads 6 -max_target_seqs 1 -outfmt 6
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