I have a genome sequence for a bacterial strain with an ORF that I'm sure encodes for a luxR gene (or similar), so a transcriptional regulator. I've also found the start and stop codon, but am having trouble finding the ribosome binding site (i.e. the Shine-Dalgarno sequence). I know typically it's AGGAGG, and that it does not always have to be so, but I'm unsure how 'different' it can be from the general consensus. Either way, I cannot seem to find a RBS. The closest I've managed to find is GAGAG, but I'm still uncertain about whether it could even be the RBS and am now starting to wonder if the ORF I have found even encodes for a real gene.
I also know that a RBS is only present if the gene encodes for a functional protein, but I can't find information on the gene encoding for rRNA or tRNA anyway.
