GREMLIN Database
DKSA - RNA polymerase-binding transcription factor DksA
UniProt: P0ABS1 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10230
Length: 151 (121)
Sequences: 1859 (1005)
Seq/√Len: 91.4

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
117_C138_C4.4191.00
41_R107_E4.3121.00
117_C135_C4.1091.00
48_R100_E3.5831.00
39_H127_E2.9351.00
36_Q123_I2.9321.00
135_C138_C2.9201.00
37_L106_V2.8021.00
115_E133_D2.7851.00
48_R96_I2.4231.00
43_I127_E2.1291.00
102_T105_K2.1141.00
41_R45_E2.0061.00
116_S134_L1.9191.00
38_A41_R1.8791.00
139_K142_A1.8451.00
47_W95_L1.7981.00
31_Y122_G1.7491.00
33_N36_Q1.7281.00
32_M40_F1.7271.00
48_R52_R1.6661.00
37_L109_E1.6091.00
44_L99_I1.6071.00
40_F123_I1.5821.00
101_K105_K1.5821.00
98_K133_D1.5001.00
81_E84_L1.4731.00
104_K108_D1.4400.99
116_S138_C1.4290.99
42_R46_A1.4270.99
38_A45_E1.3810.99
34_E38_A1.3670.99
40_F106_V1.3660.99
52_R100_E1.3400.99
124_R127_E1.3360.99
45_E49_N1.3220.99
49_N53_D1.2740.99
51_L96_I1.2680.99
47_W50_Q1.2660.99
46_A49_N1.2610.99
98_K129_R1.2470.98
43_I47_W1.2180.98
34_E109_E1.2010.98
117_C137_D1.1850.98
116_S142_A1.1650.98
105_K115_E1.1280.97
115_E134_L1.1090.97
54_E92_E1.0660.96
95_L98_K1.0650.96
27_P30_E1.0610.96
45_E48_R1.0590.96
134_L142_A1.0560.96
32_M123_I1.0350.95
103_L107_E0.9990.94
68_N71_D0.9910.94
39_H43_I0.9830.94
38_A42_R0.9800.94
73_V77_A0.9570.93
32_M39_H0.9560.93
101_K133_D0.9550.93
95_L131_T0.9420.92
129_R139_K0.9310.92
104_K107_E0.9130.91
95_L139_K0.9110.91
36_Q40_F0.8930.90
45_E103_L0.8920.90
42_R45_E0.8890.90
114_C138_C0.8790.89
58_T89_R0.8780.89
53_D57_R0.8760.89
56_D60_T0.8680.89
105_K133_D0.8650.88
26_K29_E0.8570.88
51_L92_E0.8540.88
66_A71_D0.8350.87
32_M36_Q0.8330.86
72_P132_A0.8100.85
60_T63_Q0.8070.85
96_I100_E0.8030.84
48_R99_I0.7910.83
90_D93_R0.7860.83
72_P76_A0.7850.83
102_T126_L0.7790.83
88_N92_E0.7770.82
98_K146_E0.7720.82
76_A80_E0.7610.81
95_L129_R0.7550.81
31_Y113_Y0.7520.80
136_I140_T0.7440.80
81_E106_V0.7420.79
26_K30_E0.7380.79
139_K146_E0.7190.77
70_P74_D0.7160.77
119_V137_D0.7120.77
70_P80_E0.7080.76
90_D94_K0.7070.76
30_E34_E0.7010.75
72_P78_Q0.6960.75
59_V93_R0.6960.75
60_T73_V0.6880.74
40_F122_G0.6880.74
86_L93_R0.6870.74
46_A50_Q0.6830.74
73_V80_E0.6820.73
49_N52_R0.6800.73
101_K104_K0.6790.73
75_R87_R0.6790.73
53_D56_D0.6750.73
75_R79_E0.6730.72
37_L41_R0.6660.72
141_L144_I0.6640.71
80_E83_S0.6630.71
87_R95_L0.6610.71
93_R97_K0.6580.71
51_L54_E0.6560.70
91_R95_L0.6510.70
46_A52_R0.6510.70
41_R106_V0.6470.69
62_M65_E0.6420.69
72_P96_I0.6390.69
47_W59_V0.6360.68
92_E101_K0.6350.68
68_N72_P0.6320.68
138_C143_E0.6280.67
69_F72_P0.6280.67
134_L139_K0.6240.67
111_F132_A0.6180.66
70_P73_V0.6180.66
28_G42_R0.6100.65
79_E87_R0.6020.64
91_R139_K0.6000.64
87_R98_K0.6000.64
41_R103_L0.5950.63
52_R55_V0.5910.62
82_F122_G0.5860.62
38_A136_I0.5840.62
102_T133_D0.5820.61
137_D141_L0.5810.61
26_K77_A0.5810.61
129_R146_E0.5800.61
54_E57_R0.5800.61
72_P77_A0.5770.61
47_W75_R0.5750.60
132_A139_K0.5750.60
72_P82_F0.5680.59
40_F126_L0.5580.58
87_R129_R0.5570.58
110_D113_Y0.5560.58
77_A80_E0.5550.58
114_C136_I0.5550.58
117_C120_E0.5540.58
90_D97_K0.5530.57
98_K131_T0.5490.57
67_A97_K0.5470.57
32_M76_A0.5450.56
140_T144_I0.5440.56
142_A146_E0.5430.56
32_M37_L0.5420.56
87_R146_E0.5410.56
50_Q54_E0.5400.56
103_L124_R0.5400.56
117_C140_T0.5350.55
65_E73_V0.5350.55
57_R64_D0.5310.54
77_A84_L0.5300.54
73_V76_A0.5270.54
71_D84_L0.5250.54
79_E90_D0.5220.53
113_Y123_I0.5220.53
35_A42_R0.5160.52
66_A110_D0.5150.52
48_R53_D0.5120.52
136_I139_K0.5120.52
79_E91_R0.5100.52
51_L99_I0.5080.51
60_T145_R0.5070.51
47_W88_N0.5070.51
66_A69_F0.5060.51
53_D104_K0.5050.51
91_R131_T0.5020.50
88_N102_T0.5010.50
111_F126_L0.5000.50
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
1tjlA 2 0.9603 100 0.189 Contact Map
4ijjA 1 0.8609 100 0.25 Contact Map
2kq9A 1 0.7417 99.9 0.359 Contact Map
2kgoA 1 0.4901 99.8 0.501 Contact Map
2lo3A 1 0.2914 43.5 0.914 Contact Map
3u6pA 1 0.8543 29.6 0.921 Contact Map
3mhsE 1 0.5629 26.5 0.923 Contact Map
1k82A 1 0.8808 25.5 0.924 Contact Map
3pwfA 4 0.7682 23.1 0.925 Contact Map
1lkoA 3 0.8609 19.7 0.928 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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