Table 1.
Summary of Re-annotations.
Fig 1.
Sequence of 3’ 37 nucleotides of E. coli 16S rRNA gene.
The last 24 nucleotides of helix 45 are in italics (yellow box), followed by the 13 nucleotide “tail” (underlined, red box). The anti-Shine-Dalgarno sequence CCTCCT is underlined and in bold. The terminal 3’ “A” residue is indicated with an asterisk. The 10 genomic nucleotides following the end of the tail are shown in lower case (blue box). The overall positioning of this region of the 16S rRNA is indicated (red line).
Fig 2.
In A and B, 24 bases of helix 45 are boxed in yellow; the last 13 bases of the 16S rRNA are boxed in red, and the 10 bases in the genome following the 3’ end of the 16S rRNA are boxed in blue. A. The 12,426 16S rRNAs missing the antiSD as currently annotated and corrected here, aligned by helix 45. B. 8,069 16S rRNAs which include the antiSD as currently annotated, aligned by helix 45. C. The same 8,096 16S rRNAs as in B, but aligned by the 3’ end of the current annotation.
Table 2.
Sequences of 13 base tails.
Table 3.
For CCTCCT antiSDs, examples of Shine-Dalgarno motifs.
Table 4.
Presence of Tompa Shine-Dalgarno as function of antiSD.
Fig 3.
Phylogenetic tree (low resolution) showing the distribution of the 128 species that lack a CCUCCU antiSD in their 13 b tails. Green lines indicate the phylogenetic positions of the 15 species previously identified by Lim et al. (2012) (and also identified here); orange lines show the other 113 species uniquely identified here. Because of the low resolution of this tree, individual species are not visible (i.e., there are fewer than 128 colored lines).
Table 5.
Multiple 16S rRNA genes in Alteromonas species.