I am not sure if I understand well your question but you have sequenced 16S data with Illumina, so I don't see the need for finding genes there because you only have one gene, and particularly the V3/V4 regions of the 16S gene. So unless you have also done a WGS metagenomic sequencing you don't need Prodigal at all. 

If that is the case, you probably need first to know if your sequencing was paired-end or not. If it was, then you need to merge your paired sequences in the fastq files. A software that I have used for this is Pandaseq (https://github.com/neufeld/pandaseq), but there are plenty of other options too. After this you might probably want to find Operational Taxonomic Units (OTUs) on your data, which is a form of clustering if want to use that word. 

I hope that helps, but if I misinterpreted your question please let me know.