Sequence composition of the Sigma-54 Enhancer Binding Proteins. A) The 'GAFTGA' sequence logo of the 4970 putative functional Sigma-54 related EBPs. Data from literature and similarity in chemical structure were used to categorize the substitutions into those that relate to functional EBP54s, those that will probably relate to functional EBP54s, and those that will abolish the interaction with Sigma-54. The effect of amino acid substitutions on the EBPs capacity to activate Sigma-54 mediated transcription has been studied by [75, 76]. Furthermore, some experimentally validated activators carry specific substitutions: G1 is replaced by N in the only EBP54 of Paracoccus denitrificans and Ruegeria pomeroyi (putative: ADEHS); A2 is replaced by S in LevR of the Bacilli (putative: TGIVMC; inactive: DN); F3 is replaced by Y in TouR of Pseudomonas stutzeri (other replacements inactive); T4 is replaced by S in BkdR of B. subtilis and by E in PhhR of Pseudomonas aeruginosa (putative: D; other replacements inactive); G5 is replaced by D in FlgR, the only EBP54 of Campylobacter and other Epsilon-proteobacteria (putative; EAHNS); and A6 is replaced by S in PrpR of E. coli (putative: TGIVMC; inactive DN). B) Schematic representation of the four basic architectures of functional EBP54s. The types were distinguished on basis of their domain organization: Ia) N-terminal signal recognition domain of the response regulator (RR) type, followed by the central activator domain and a C-terminal DNA-binding domain of the HTH_8 PFAM family; Ib) different N-terminal signal recognition domain(s), followed by the central activator domain and a C-terminal DNA-binding domain of the HTH_8 PFAM family; Ic) an activator domain, but lacking the signal recognition domain (e.g. PspF, HrpRS, LafK) or the DNA-binding domain (e.g. CtcC, FlgR) or both (FleT); and II) N-terminal DNA-binding domain of the NtrC family, the central domain, and four phosphorylatable domains related to the PTS.