Figure 6

Amino acids conservation between σ⁵⁴ Enhancer Binding Proteins (EBP) and AoxR. Sequence alignment was performed with ClustalW. The conserved amino acids are presented with a blue background and the blue intensity reflects sequence similarities. Only the central binding domain is indicated. Region CI has remarkable similarity to the consensus glycine-rich flexible loop motif (Walker A - consensus motif GxxGxGK), and also contains hydrophobic residues. Region CII is hydrophobic. The region CIII is predicted to fold into two alpha helices separated by a turn. This region is involved in a specific interaction between the EBP and the Eσ⁵⁴ required for open promoter complex formation via the GAFTGA motif. Region CIV is rich in glycine, negatively charged and contains a consensus sequence of 4 aliphatic residues followed by 2 negatively charged residues (Walker B - consensus motif TVFLDE); in contrast, CVI is positively charged and is rich in aromatic residues and proline. Region CV is found about 80 amino acids away from region CI, and has a consensus sequence QakLLRVLqe. Finally, region CVII has a core of eight highly conserved amino acids. Sequence informations of other genes were obtained from Colibri database (Institut Pasteur, Paris).