Figure 2.

Riboswitch candidates crcB, yjdF, wcaG, manA, pfl, epsC, and ykkC-III. Annotations are as described in Figure 1a. The transcription terminators that often overlap crcB or pfl RNAs are not depicted because they are not consistent in all representatives. They are annotated in Additional File 3. Question marks signify base-paired regions ("P4?" in yjdF, "P2?" in pfl, and "pseudoknot?" in manA) with weaker covariation or structural conservation. The pseudoknot in the epsC motif was predicted by others (Wade Winkler, personal communication, 2009). A portion of this figure was adapted from the supplementary data of a previous publication [21].