Analysis of covariation in LT helices of 16S rRNA. (A) Each taxonomic class was analyzed independently. The LT sequences from species belonging to the class were compiled. Sequences sharing sequence similarity were clustered together using the MMSeqs easy-cluster function to reduce RNAClust computational burden and to generate realistic consensus structures. For each sequence cluster, RNAClust was run to determine the consensus structure and its covariation. The same SSW approach as for the shuffling method was applied. The fraction of LT bps exhibiting covariation (e.g., non-red colored bps) was computed. (B) The RNAClust consensus structure rooted at Staphylococcus piscifermentans. The consensus structure creates large loops where structure is not conserved, typically far away from the LT stem and mature rRNA (upper left area). Color-coding indicates the number of different base pairs observed at a given position: red, 1; yellow, 2; green, 3; cyan, 4; blue, 5; magenta, 6. Tint level reflects the fraction of mismatches (full color indicating no mismatches, followed by a lighter tint up to 10% mismatches, even lighter for up to 20% mismatches, and no coloring for above 20% mismatches). (C) The distribution of all SSW scores, where the black dotted line corresponds to the threshold used to distinguish LT sequences with evidence for a stem from LT sequences without such evidence. (D) Histogram showing the degree of covariation across all structures, where the black dotted line corresponds to the threshold that distinguishes weak from strong covariation.
