Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function
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.
