Functional MarA binding domain variants selected against different binding sites.

Each row represents a different MarA protein variant that will initiate transcription in our selection system. ‘BS’ is the binding site the MarA variant was selected against. The three letters correspond to the bases at position , and in the mar binding site (Figure 1, Figure 2B). ‘42-45-46’ are the residues at positions 42, 45 and 46 in the selected MarA variants (Figure 2C). ‘Tet-20’ and ‘Tet-30’ are the number of colonies selected at that tetracycline concentration that contained that variant. ‘Total’ is the sum of ‘Tet-20’ and ‘Tet-30’. ‘Codons’ are the number of different codons sets that specified that variant. An ‘X’ in the ‘Best’ column identifies the variant that had the highest affinity for a given binding site as determined by a competition experiment. An ‘X’ in the ‘MITOMI’ column identifies the protein variants whose binding we characterized by MITOMI (Figure 4) and by an in vivo binding site selection (Figure 7). The variant that corresponds to the wild type protein (WQR) is bolded.