The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons

Each row lists data for an E. coli transcription factor where the crystal structure and information about residues that are important for DNA binding specificity are available. We list the literature reference and our evaluation of the conservedness of these residues for each species. A plus (minus) sign denotes conserved (not conserved), a question mark stands for unclear cases (for example, a frame shift inside the binding domain). The selected residue sets are AraC (Rhee et al. 1998): A198, S199, V200, A201, Q202, H203, P208-Q218, I246-V253, Q258-T268; Crp (Parkinson et al. 1996): K27, V140, K167, R170, Q171, S180, R181, E182, T183, R186, K189, H200; MetJ (Somers and Phillips 1992): G16, K18, K23, K24, T26, R41, N54, S55; OmpR (Martinez-Hackert and Stock 1996): R150, T162, K170, R182, S200, V203, M211, V212, R220, T224, G229 RpoD (Malhotra et al. 1996) Y425, Y430, W433, W434, Q437, T440, R441; SoxS (Rhee et al. 1998): D25-K30, K35-T46, I73-L80, Q85-Q96; TrpR (Otwinowski et al. 1988): Q68, R69, L71, K72, L75, A77, G78, I79, A80, T81, I82, T83, R84, G85, S86, N87, L89, K90. Additional details, including the complete alignments, can be found on our website.