Figure 1.

Multiple alignment of the Mj0882, RsmC, RsmD, and YbiN families. Sequences are denoted by the species' name and the NCBI gene identification number; sequences lacking the number were obtained from the unfinished genome data. Numbers on the left side indicate the index of the first N-terminal residue shown, numbers in parentheses indicate how many residues in an insertion were omitted for clarity. Conserved motifs are labeled according to the nomenclature described for the AdoMet-dependent MTase superfamily [12]. Conserved residues are highlighted in black; the residues with invariant physicochemical character (hydrophobic, small etc.) are highlighted in gray. Conserved carboxylates predicted to bind AdoMet are shown in black on red background; the pair of residues proposed to make van der Waals contacts to guanine is shown in green on a yellow background; the Asn residue (His in Archaeal YbiN orthologs) proposed to catalyze the methyltransfer is shown in yellow on red background; the carboxylate proposed to bind the ribose of the target nucleoside is shown in yellow on magenta background. Secondary structure elements of Mj0882, extracted from the 1dus coordinates and virtually identical for the secondary structure independently predicted for other families (see Methods), are shown above the alignment.