Figure 6. Consensus alignment of long RSH and small RSH subgroups across the ppGpp synthetase and hydrolase domains, with Rel_Seq NTD structure colored according to conservation patterns in the alignment.

A) Alignment of RSH NTD sequences at the 70% level. Yellow highlighting shows those residues that are only conserved only in long RSHs. Blue and red boxes show sites of the HD and SYNTH nucleotide binding pockets, respectively. Bright turquoise and orange boxes show the location of surface residues in the SYNTH and HD domains respectively that are likely to be involved in inter molecular interactions, or interactions with the CTD in long RSHs. The box is dotted where the region is disordered in the structure. The pale marine box shows those regions that appear to be involved in HD-SYNTH interactions. Arrows show especially interesting sites (see inset box in B). The orange bar above the alignment shows the location of the differentially conserved motif of [44]. B) Structure of the Rel[HS] protein from S. equisimilis (Rel_Seq) [40], colored according to the conservation patterns of the alignment in A. The inset box shows a subset of particularly interesting sites (labeled with arrows in A). Residue numbering is as in Rel_Seq, followed by alignment coordinates from A in parentheses.