Fig. 1

Improvised search model to predict ANTAR-target RNAs in actinobacteria. A Cartoon showing the ANTAR protein-RNA regulatory system. Specific signals activate the ANTAR protein (grey), which upon activation binds the dual stem loop ANTAR-target RNA (blue). This results in regulation of the downstream gene (gene linked to ANTAR-target RNA, shown in purple). B Schematic shows the steps performed to identify ANTAR-target RNAs using a covariance-based computational search. Previously reported search models with too little diversity (focused) did not yield any results in actinobacteria, while a search model with only moderate diversity (partially focused) identified ~ 243 RNAs in actinobacteria, with a bit score threshold≥14. 30 actinobacterial representative RNAs from this set were used to enrich the search model further and this actionbacteria centric search model (diffused search model) resulted in a comprehensive list of ANTAR-target RNAs in actinobacteria. The probability of finding RNAs in actinobacteria is represented as a bar (red indicates high probability). C Bar plot (left) shows the total number of actinobacterial genomes where RNAs are predicted using three different search models (purple, gray and green). Bar plot (right) shows the total number of RNAs predicted using three different search models. The diffused search model is able to predict RNAs in more than 60% of actinobacterial genomes as compared to the focused and partially focused search model. D RNA sets from firmicutes/ proteobacteria and actinobacteria were clustered using cmbuild. Bar plot shows the number of clusters obtained with varying sequence identity cut-offs imposed using cmbuild. Clusters obtained using 51–54% sequence identity cut-off are shown as an inset. E Consensus structure obtained for the actinobacterial ANTAR-target RNA sequences from the largest cluster with 55% sequence identity is visualized using Forna (Left). Stems (green) while the internal loops (blue) and the unpaired nucleotides (pink) are shown. Parameters obtained from RNAz for the largest cluster with 55% sequence identity are shown (Right)