We examined 20,648 prokaryotic unique taxids with respect to the annotation of the 3’ end of the 16S rRNA, which contains the anti-Shine-Dalgarno sequence. We used the sequence of highly conserved helix 45 of the 16S rRNA as a guide. By this criterion, 8,153 annotated 3’ ends correctly included the anti-Shine-Dalgarno sequence, but 12,495 were foreshortened (or otherwise mis-annotated), missing part or all of the anti-Shine-Dalgarno sequence, which immediately follows helix 45.

We re-annotated, giving a total of 20,648 16S rRNA 3’ ends. The vast majority indeed contained a consensus anti-Shine-Dalgarno sequence, but 128 organisms seemed to have either a variant anti-Shine-Dalgarno, or no recognizable anti-Shine-Dalgarno, in their 16S rRNA(s). For these 128 organisms, and also for 222 example organisms containing a consensus anti-Shine-Dalgarno, we identified the Shine-Dalgarno-like motifs actually enriched in front of each organism’s open reading frames, to see how Shine-Dalgarno motifs correlated with anti-Shine Dalgarno motifs.

In general, organisms lacking a perfect anti-Shine-Dalgarno motif also lacked a recognizable Shine-Dalgarno, while for organisms containing anti-Shine-Dalgarno motifs, a variety of results were obtained. The fact that some organisms do not seem to have or use Shine-Dalgarno motifs implies that prokaryotes must have other robust mechanisms for recognizing AUG Start codons for translation.