Fig. 6

Representatives of various types of predicted structured nucleic acid motifs discovered among five bacterial genomes. a-e Sequence and predicted secondary structure models for representative ‘named’ motifs identified among the five bacterial genomes examined in this study. Extended blue shading in a and b designate possible short ORFs. For the translated WebLogo consensus sequence in a, amino acids in blue, green, and black are hydrophilic, neutral, and hydrophobic, respectively. The two candidate uORFs in b are associated with shikimate metabolism genes, and notable amino acids related to this pathway and encoded by the uORFs include phenylalanine [F] and tyrosine [Y]. The protein binding candidate in c is depicted with two pyrimidine-rich sequences highlighted that might function as protein binding sites. In addition to the type I consensus depicted, representatives conforming to a type II (only one hairpin-loop similar to P3) and a type III (terminator stem only) consensus also exist. RBS designates ribosome binding sites. Additional annotations are as described in the legend to Fig. 3. f Comprehensive summary of the fate of the unknown IGRs after analysis of the five bacterial genomes examined in this study. Annotations are as described in the legend to Fig. 2c