Figure 1

α-Proteobacterial RNA elements. (a) Consensus sequences and structures. Red and black positions for each RNA element indicate >95% and >80% conservation of a particular nucleotide, respectively. Purine (R) or pyrimidine (Y) designations are used when a single nucleotide is not >80% conserved. Solid black lines indicate variable regions, and solid grey lines are optional sequence insertions that are not present in all examples of an element. Circles represent single nucleotides whose presence (but not sequence) is conserved. Base pairs supported by strong (both bases in the pair vary) and weak (only one base in the pair varies) sequence covariation in a motif alignment have green and blue shaded backgrounds, respectively. (b) Phylogenetic distributions. Element names are chosen based on the proximity that representatives from A. tumefaciens have to genes.