Fig. 2

Models and structural features of GGDEF, EAL and hybrid proteins from the A. brasilense Sp7 genome. a Diguanylate cyclase domain structures from the A. brasilense Sp7 genome. The structures shown correspond to the 20 conserved DGCs sequences indicated in Table 4 in comparison to the crystal structure of WspR (PDB id: 3BRE; red) from P. aeruginosa [47]. The domain surface representations are labeled in white, and the bound ligand is labeled in green. The WebLogo sequence [78] is based on the PFAM alignments, which show conserved GG[D/E]F motifs and are colored green-red. b. Domain structures of phosphodiesterase from the A. brasilense Sp7 genome. The structures shown correspond to the five conserved PDE-EALs indicated in Table 4 in comparison to the crystal structure of PdeA (PDB ID: 3U2E; red) from C. crescentus [48]. The domain surface representations are labeled in white, the bound ligands (EAL domain) are shown in yellow, and loop 6 is colored green. The WebLogo sequence [78] is based on the PFAM alignments, which show a conserved motif. The red arrow indicates the visible discrepancies in the 3U2E crystallographic structure. c. Structures of the hybrid proteins from the A. brasilense Sp7 genome. The structures shown correspond to the nine hybrid sequences indicated in Table 4 in comparison to the crystal structure of WspR (PDB id: 3BRE; red) from P. aeruginosa [47]. The domain surface representations are labeled in white, and the bound ligand is labeled in green. The WebLogo sequence [78] is based on the PFAM alignments, which show a conserved GG[D/E]F motifs and are colored green-red. The structures shown correspond to the nine conserved PDE-EALs indicated in Table 4 in comparison to the crystal structure of PdeA (PDB ID: 3U2E; red) from C. crescentus [48]. The domain surface representations are labeled in white, the bound ligands (EAL domain) are shown in yellow, and loop 6 is colored green. The WebLogo sequence [78] is based on the PFAM alignments, which show a conserved EAL motif. The red arrow indicates the visible discrepancies in the 3U2E crystallographic structure