Figure 3.

Contextual connections of ATP-grasp ligase-based and related RNA repair systems. (A) Contextual network constructed as described in Supplementary Material. Protein domain nodes are colored according to general functional category. Phosphoesterase/phosphotransferase domains are further demarcated by dotted orange box. (B–Q) Representative depictions of conserved domain architectures and gene neighborhoods. Domain architectures are depicted as adjoining shapes, not drawn to scale. Gene neighborhoods are depicted as directed boxes, genes within neighborhood encoding multiple domains contain individually-colored boxes for each domain. All contexts are labeled with organism name and NCBI gene identifier (gi) number. Green lettering: phyletic distributions for each group of systems. Blue dots: novel predicted RNA repair systems or systems containing a previously-unrecognized component. (R–X) Representatives of conserved domain architectures and gene neighborhoods containing the MJ1316 domain. All domain and organism expansions are provided in Supplementary Material.