JMMB Supplementary Material

Figure 6B

Figure 6. (A) Alignment of the N-termini of 80 Rel, RelA and SpoT proteins around motifs I and II of the HD domain (Aravind and Koonin, 1998). The sequences SpoT Pfr, SpoT ?, CsrS Vsp and SpoT Lpn were not included in the alignment. The RelA proteins are separated from the Rel and SpoT proteins by a line indicating the location of conserved residues "H" in motif I and "HD" in motif II. Note that these amino acids are conserved in Rel and SpoT proteins but RelA proteins carry substitutions at the conserved residues. The Rel1 and Rel2 of P. gingivalis proteins are placed at the intersection between the Rel and RelA proteins. (B) Alignment of the N-termini of 80 Rel, RelA and SpoT proteins around motif V of the HD domain (Aravind and Koonin, 1998). The RelA proteins are separated from the Rel and SpoT proteins by a line indicating the location of the conserved residue "D" in this motif. Note that this amino acid is conserved in Rel and SpoT proteins. With the exception of Rel2 Pgi, RelA proteins carry substitutions of this residue.

Figure 7. (A) Alignment of the C-terminus of RpoB proteins. The common motif in purine nucleotide-binding proteins (GXXXXGK) (Glass et al., 1986; la Cour et al., 1985) is indicated by asterisks. A crosslinked ppGpp derivate was found in a fragment consisting of residues 802-1211, 1216 or 1223 of the E. coli RpoB protein (Chatterji et al., 1998). At the end of the first column, the presence/absence of a ppGpp synthetase/hydrolase in the completely sequenced genomes is indicated. (B) Alignment of the N-terminus of RpoC proteins. A crosslinked ppGpp derivate was found in a fragment consisting of residues 29-102 of the E. coli RpoC protein (Toulokhonov et al., 2001).