GREMLIN Database
YBAQ - Uncharacterized HTH-type transcriptional regulator YbaQ
UniProt: P0A9T6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13245
Length: 113 (91)
Sequences: 1569 (1129)
Seq/√Len: 118.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
33_L62_V2.5801.00
60_A67_V2.3321.00
40_S55_M2.2721.00
72_N76_A2.1711.00
28_N32_E2.1301.00
29_E33_L2.1031.00
17_Y21_E2.0991.00
27_I42_S1.9791.00
28_N38_R1.9791.00
43_A49_R1.9681.00
39_N42_S1.9421.00
6_R80_W1.8801.00
60_A66_T1.7431.00
60_A65_T1.6951.00
39_N43_A1.6871.00
16_L21_E1.5931.00
42_S46_N1.5891.00
56_A68_D1.5741.00
30_L41_V1.5641.00
77_V81_E1.5561.00
20_L30_L1.5281.00
86_M92_L1.4601.00
62_V95_I1.4431.00
35_H94_R1.3981.00
80_W84_N1.3861.00
61_K97_T1.3611.00
8_P81_E1.3541.00
44_L51_L1.3301.00
36_V55_M1.2861.00
27_I39_N1.2761.00
43_A48_N1.2590.99
67_V83_E1.2580.99
67_V79_L1.2320.99
38_R42_S1.2320.99
8_P80_W1.2160.99
6_R9_T1.2000.99
54_E58_R1.1980.99
44_L55_M1.1920.99
13_D17_Y1.1590.99
27_I41_V1.1480.99
65_T69_F1.1470.99
19_Y22_P1.1470.99
68_D83_E1.1430.99
14_I73_L1.1230.99
57_F82_V1.1200.99
27_I45_I1.1100.99
37_H40_S1.0730.98
87_R93_G1.0690.98
56_A67_V1.0660.98
16_L47_N1.0640.98
71_L75_A1.0640.98
72_N75_A1.0460.98
52_T55_M1.0440.98
25_L30_L1.0390.98
50_K78_D1.0120.97
27_I38_R0.9860.97
10_T47_N0.9830.97
16_L45_I0.9610.97
30_L59_L0.9470.96
56_A60_A0.9410.96
27_I43_A0.9370.96
13_D47_N0.9290.96
15_L19_Y0.9110.95
39_N46_N0.9030.95
9_T80_W0.8910.95
57_F92_L0.8740.94
22_P69_F0.8730.94
86_M91_E0.8650.94
5_T9_T0.8600.94
66_T69_F0.8390.93
56_A72_N0.8330.92
40_S49_R0.8260.92
20_L23_L0.8170.92
68_D72_N0.8020.91
14_I65_T0.7950.91
69_F73_L0.7910.90
92_L95_I0.7890.90
10_T50_K0.7860.90
76_A80_W0.7800.90
7_K81_E0.7560.88
82_V86_M0.7540.88
15_L44_L0.7400.87
10_T77_V0.7400.87
13_D18_E0.7390.87
91_E94_R0.7350.87
87_R90_E0.7300.87
14_I18_E0.7220.86
49_R55_M0.7180.86
9_T14_I0.7060.85
11_P77_V0.6940.84
29_E32_E0.6920.84
65_T70_W0.6850.83
25_L29_E0.6640.81
27_I49_R0.6610.81
36_V40_S0.6610.81
69_F72_N0.6550.80
30_L34_L0.6500.80
36_V41_V0.6470.79
32_E46_N0.6410.79
43_A63_F0.6400.78
33_L63_F0.6340.78
16_L46_N0.6190.76
53_T71_L0.6180.76
16_L22_P0.6100.75
56_A71_L0.6100.75
81_E84_N0.6030.74
7_K84_N0.5880.72
33_L93_G0.5880.72
59_L70_W0.5770.71
11_P47_N0.5740.71
19_Y65_T0.5680.70
26_K29_E0.5660.70
19_Y63_F0.5650.69
40_S58_R0.5630.69
28_N39_N0.5600.69
75_A78_D0.5580.68
14_I19_Y0.5500.67
90_E94_R0.5480.67
34_L59_L0.5450.67
59_L63_F0.5400.66
18_E69_F0.5370.66
51_L59_L0.5340.65
86_M90_E0.5250.64
40_S54_E0.5240.64
26_K32_E0.5210.63
20_L25_L0.5190.63
75_A79_L0.5190.63
36_V58_R0.5170.63
18_E22_P0.5140.62
33_L61_K0.5110.62
84_N91_E0.5070.61
91_E96_E0.5070.61
60_A72_N0.5040.61
9_T70_W0.5030.61
82_V85_N0.5010.60
56_A65_T0.5000.60
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  
2ebyA 2 0.9027 99.7 0.554 Contact Map
3cecA 1 0.8053 99.6 0.6 Contact Map
3trbA 3 0.8142 99.6 0.601 Contact Map
4mctA 2 0.823 99.6 0.608 Contact Map
2ictA 2 0.8319 99.5 0.635 Contact Map
4mcxA 2 0.823 99.5 0.64 Contact Map
2b5aA 2 0.6814 98.9 0.719 Contact Map
3fmyA 2 0.5752 98.9 0.721 Contact Map
4yarA 2 0.9912 98.9 0.723 Contact Map
4pu7B 2 0.5929 98.8 0.728 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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