Table 2: Matrix of equivalent residue pairs of available AraC/XylS 3D structures(a).

1bl0 1xs9 1d5y 3oou 2k9s 3gbg 3mkl 3mn2 3oio 3lsg 1u8b 1wpk 1zgw 1bl0 100 100 100 96 84 81 88 82 94 97 47 44 42 1bl0 0.0 0.7 0.9 1.8 1.9 2.2 1.9 2.2 1.9 1.3 1.6 2.2 2.3 100% 100% 50% 18% 16% 15% 16% 14% 19% 25% 15% 13% 15% 1xs9 100 100 93 82 78 88 84 93 97 48 45 45 1xs9 0.0 1.1 1.7 1.8 2.0 1.8 2.0 1.7 1.4 1.7 2.3 2.3 100% 50% 18% 16% 15% 16% 14% 19% 25% 15% 13% 15% 1d5y 100 95 80 81 88 88 95 97 45 44 41 1d5y 0.0 1.5 1.7 2.1 1.8 2.0 1.8 1.2 1.7 2.3 2.3 100% 20% 21% 16% 11% 16% 21% 25% 25% 18% 17% 3oou 100 72 84 87 88 87 97 47 42 37 3oou 0.0 2.0 2.3 1.8 1.8 1.9 1.4 1.7 2.3 2.3 100% 23% 16% 17% 20% 20% 31% 15% 13% 11% 2k9s 101 89 91 84 95 86 45 41 33 2k9s 0.0 2.0 2.0 2.3 1.8 1.9 2.1 2.3 2.6 100% 21% 24% 22% 25% 26% 23% 10% 9% 3gbg 99 90 84 95 81 35 36 23 3gbg 0.0 1.5 2.2 1.6 2.0 2.3 2.4 2.6 100% 28% 15% 20% 23% 8% 3% 6% 3mkl 99 96 95 88 45 32 35 3mkl 0.0 1.7 1.3 1.7 1.9 2.4 2.5 100% 21% 26% 23% 19% 10% 8% 3mn2 102 100 85 44 40 28 3mn2 0.0 1.6 2.0 2.1 2.2 2.8 100% 28% 15% 21% 12% 13% 3oio 100 93 51 45 35 3oio 0.0 1.8 2.0 2.0 2.7 100% 18% 33% 22% 21% 3lsg 100 45 48 41 3lsg 0.0 1.5 2.4 2.2 100% 15% 13% 19% 1u8b 52 41 36 1u8b 0.0 2.5 2.2 100% 62% 44% 1wpk 60 28 1wpk 0.0 2.5 100% 28% 1zgw 53 1zgw 0.0 100%

(a)The top number indicates the number of equivalent positions of the aligned structures (length of the alignment). The middle number denotes the root mean square (RMS) deviation of equivalent atoms (3.5 Å distance cutoff) and the lower number denotes the sequence identity of equivalent residues. Structures were aligned with SALIGN [16]. Structures of unknown biological role are indicated in bold.