GREMLIN Database
YOBU - Putative transcriptional regulator protein YobU
UniProt: O34637 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 160 (149)
Sequences: 983 (802)
Seq/√Len: 65.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
134_T157_A5.1241.00
39_Q43_Q3.1661.00
18_S74_T3.1471.00
130_L159_K3.0351.00
12_K96_L2.9401.00
64_N74_T2.9051.00
63_S76_S2.8631.00
22_S72_F2.5681.00
13_R95_D2.2471.00
11_L98_A2.2051.00
11_L95_D2.0941.00
108_I151_Q2.0431.00
101_Y137_F1.9861.00
8_H100_A1.8841.00
110_P113_E1.8821.00
104_F156_V1.8791.00
122_I154_I1.8581.00
106_S152_V1.8271.00
38_D42_K1.7871.00
20_R72_F1.7721.00
19_Q39_Q1.7411.00
62_Y65_Y1.7190.99
135_G157_A1.6860.99
102_A125_W1.6660.99
113_E117_E1.6190.99
14_F61_L1.6170.99
144_A147_P1.6130.99
118_T122_I1.5540.99
10_D98_A1.5200.99
22_S27_M1.5100.99
105_T151_Q1.5010.99
15_A81_Q1.5000.99
104_F125_W1.4950.99
36_L77_V1.4870.99
19_Q36_L1.4790.98
131_R136_D1.4400.98
32_R35_A1.4340.98
66_E71_G1.4290.98
64_N94_I1.4260.98
15_A91_Y1.4000.98
99_S134_T1.3990.98
49_L81_Q1.3910.98
123_W131_R1.3620.97
126_D129_H1.3490.97
62_Y123_W1.3290.97
13_R93_N1.3080.97
23_N123_W1.3010.97
121_E124_T1.2800.96
60_A77_V1.2740.96
105_T153_N1.2720.96
10_D85_D1.2570.96
27_M32_R1.2490.96
123_W136_D1.2430.95
12_K80_F1.2250.95
109_G112_E1.2010.95
69_T133_F1.1960.94
9_L99_S1.1770.94
44_D47_A1.1740.94
119_W131_R1.1690.94
65_Y131_R1.1530.93
21_T136_D1.1430.93
146_V149_R1.1410.93
125_W129_H1.1170.92
18_S76_S1.1060.92
67_Q71_G1.0920.91
106_S154_I1.0900.91
115_V152_V1.0870.91
5_H103_V1.0780.91
103_V139_M1.0580.90
63_S74_T1.0470.89
76_S92_E1.0320.89
36_L75_F1.0260.88
118_T121_E1.0260.88
41_W46_S1.0240.88
132_T158_I1.0230.88
62_Y131_R1.0140.88
16_G76_S1.0120.88
61_L94_I0.9990.87
33_I104_F0.9970.87
88_P93_N0.9770.86
62_Y119_W0.9620.85
75_F140_Y0.9590.85
66_E72_F0.9440.84
34_P125_W0.9340.83
37_W79_T0.9280.83
23_N73_Y0.9270.83
60_A140_Y0.9230.82
6_I102_A0.9200.82
13_R83_Y0.9190.82
97_P135_G0.9030.81
106_S118_T0.9020.81
100_A121_E0.8980.81
14_F78_G0.8910.80
19_Q32_R0.8900.80
18_S92_E0.8850.80
142_Q154_I0.8650.78
64_N131_R0.8640.78
6_I158_I0.8550.77
125_W157_A0.8530.77
121_E125_W0.8530.77
104_F154_I0.8520.77
17_L45_M0.8380.76
20_R74_T0.8380.76
20_R66_E0.8350.76
58_I77_V0.8320.75
35_A38_D0.8290.75
54_K57_S0.8190.74
21_T131_R0.8170.74
62_Y133_F0.8120.74
84_D93_N0.8070.73
14_F76_S0.8060.73
7_T103_V0.8050.73
112_E116_L0.8040.73
28_T34_P0.8030.73
61_L67_Q0.7970.72
61_L96_L0.7910.72
40_L58_I0.7900.72
58_I62_Y0.7860.71
17_L40_L0.7790.70
37_W103_V0.7790.70
65_Y119_W0.7760.70
132_T157_A0.7730.70
15_A93_N0.7700.70
7_T158_I0.7670.69
144_A150_A0.7660.69
103_V155_Y0.7570.68
147_P150_A0.7530.68
118_T154_I0.7530.68
23_N65_Y0.7390.66
51_Q85_D0.7370.66
19_Q123_W0.7360.66
65_Y136_D0.7360.66
21_T65_Y0.7350.66
119_W136_D0.7240.65
59_I63_S0.7170.64
6_I100_A0.7150.64
60_A75_F0.7140.64
101_Y155_Y0.6990.62
17_L43_Q0.6970.62
65_Y73_Y0.6930.61
111_I114_I0.6930.61
37_W60_A0.6890.61
106_S114_I0.6860.61
106_S109_G0.6850.61
9_L137_F0.6760.60
17_L36_L0.6720.59
65_Y123_W0.6680.59
115_V154_I0.6570.57
84_D89_G0.6540.57
34_P103_V0.6530.57
104_F118_T0.6530.57
21_T73_Y0.6520.57
75_F138_E0.6510.57
109_G114_I0.6480.56
138_E154_I0.6460.56
105_T141_D0.6440.56
28_T157_A0.6340.55
57_S141_D0.6330.55
106_S119_W0.6290.54
9_L12_K0.6240.54
61_L156_V0.6230.53
30_E34_P0.6210.53
43_Q48_L0.6080.52
103_V125_W0.6080.52
61_L135_G0.6050.51
117_E120_K0.6050.51
141_D151_Q0.6000.51
56_K83_Y0.5990.51
15_A117_E0.5980.50
122_I141_D0.5960.50
17_L142_Q0.5930.50
10_D51_Q0.5910.50
79_T103_V0.5890.49
26_E31_R0.5860.49
17_L55_D0.5850.49
73_Y136_D0.5850.49
21_T119_W0.5830.49
12_K149_R0.5820.49
28_T31_R0.5770.48
79_T91_Y0.5760.48
61_L78_G0.5750.48
46_S122_I0.5740.48
141_D153_N0.5710.47
8_H98_A0.5670.47
13_R139_M0.5650.47
85_D113_E0.5640.46
40_L78_G0.5600.46
40_L43_Q0.5590.46
64_N123_W0.5570.46
35_A95_D0.5560.46
119_W126_D0.5510.45
14_F46_S0.5480.45
105_T115_V0.5470.44
85_D89_G0.5460.44
95_D130_L0.5440.44
98_A121_E0.5430.44
76_S94_I0.5410.44
28_T116_L0.5370.43
140_Y154_I0.5370.43
80_F159_K0.5360.43
15_A89_G0.5350.43
34_P111_I0.5310.43
78_G151_Q0.5300.43
83_Y158_I0.5270.42
88_P91_Y0.5260.42
123_W133_F0.5260.42
7_T11_L0.5240.42
58_I61_L0.5220.42
64_N111_I0.5210.42
81_Q106_S0.5180.41
35_A113_E0.5170.41
126_D133_F0.5160.41
59_I80_F0.5150.41
23_N131_R0.5130.41
21_T71_G0.5110.40
57_S139_M0.5090.40
34_P138_E0.5090.40
89_G92_E0.5060.40
14_F118_T0.5030.39
40_L137_F0.5020.39
23_N26_E0.5010.39
108_I150_A0.5010.39
125_W135_G0.5010.39
22_S76_S0.5000.39
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  
3gk6A 1 0.9125 100 0.407 Contact Map
3lurA 1 0.9563 100 0.431 Contact Map
1d5yA 1 0.9437 99.9 0.535 Contact Map
1jyhA 1 0.9187 99.9 0.554 Contact Map
3e0hA 1 0.925 99.9 0.579 Contact Map
1r8eA 2 0.9187 99.8 0.601 Contact Map
3b49A 1 0.9437 99.5 0.701 Contact Map
4b0yA 1 0.925 60.1 0.922 Contact Map
4h40A 2 0.3187 23.9 0.939 Contact Map
2fcgF 1 0.1562 4.7 0.955 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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