How can I find the genes which are connected with specific metabolic compound for special kind of bacteria?

There are certain locations on the genome where a mutation might happen at a higher incident. However, in bacteria the active genes are/make up almost the entire genome where the active genes in humans makes' up only 5% of the human genome. Can we say: that a preliminary ratio for the difference in mutations in active gene loci, for example, between bacteria and human is as the difference between the ratio 1:1 and 1:0.05. This difference is due to the fact that intros also play a role in diluting mutations which otherwise will be affecting active genes; the more introns there are in a given genome the lesser the chance that the active genes loci will be affected with a mutation?

I am performing 16S Metagenomic targeted sequencing to profile a mock bacterial community containing 27 bacteria species. My project requires the exact position or loci of the hypervariable regions in each of the bacteria species. I have searched all over the web for a 16S database that shows the loci of hypervariable regions, but haven't been successful. Any help would be much appreciated. I have already looked at: RDP and greengene. 

We have whole genome sequence data of Paenibacillus sp. and Arthrobacter sp. On submission of the sequence data with NCBI we got queries (a) If this is a circular genome, are the ends of the sequence contiguous around the circle with no overlap and no gap? (b) Should there be a gap at the end of the sequence? If there should be a gap, do you know the gap size or should this be an unknown length gap? 

Are they still regarded as different strains of a single pathogen or different species of Xanthomonas?

I am trying to characterize a new species of bacteria. I have a 924 bp long sequence of its ribosomal DNA which, when entered into a GC content calculator, shows a percentage of 49%. I am under the impression that 60% and over are considered high GC content. Is this enough or would further tests be necessary?

We are working on Biofilm and Quorum sensing genes of E.coli, we suggest some of reasons maybe:- Contamination, Annealing Temperature, Melting Temperature, DNA Extraction mistakes in the Techniques, we identified them by biochemical tests to be sure the isolates are E.coli, but now we are collecting samples from the beginning and doing the procedure again

In a bacteria genome I´ve found several ORF for Surface layer protein, and I suspect some are truncated copies of the gene. I would like to find if all of them have promoters.

Please suggest a company that offer bacterial genome analysis starting from submission of the genome sequence in GenBank to genome annotation, reports of gene predictions and functions etc.