GREMLIN Database
NRDR - Transcriptional repressor NrdR
UniProt: P0A8D0 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11320
Length: 149 (147)
Sequences: 1990 (1046)
Seq/√Len: 86.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
90_H115_Q5.5461.00
5_F36_E3.9441.00
80_S83_D3.5971.00
72_R75_E3.3221.00
77_R120_D3.3151.00
70_M87_A3.2981.00
70_M84_V3.0281.00
94_Q115_Q2.8151.00
143_E146_R2.5341.00
12_K32_L2.4061.00
67_R88_I2.3851.00
67_R84_V2.3701.00
8_A33_V2.2571.00
51_V108_I2.2291.00
66_L112_V2.2071.00
141_G145_A2.0971.00
54_S106_K2.0511.00
87_A119_L2.0421.00
64_E68_S1.9901.00
83_D86_M1.9691.00
98_T107_M1.9681.00
63_E92_K1.9401.00
58_R102_E1.8981.00
87_A115_Q1.7561.00
30_Q35_N1.6571.00
10_D32_L1.6171.00
83_D119_L1.5371.00
104_P107_M1.4900.99
95_L111_L1.4780.99
100_E107_M1.4760.99
87_A91_I1.4660.99
54_S133_S1.4490.99
132_R143_E1.4390.99
19_V24_S1.3750.99
69_G75_E1.3710.99
138_K142_E1.3610.99
63_E89_N1.3320.99
52_V102_E1.3270.99
94_Q114_E1.3260.99
142_E145_A1.2870.98
110_N132_R1.2640.98
24_S43_V1.2580.98
12_K69_G1.2490.98
125_I135_E1.2310.98
91_I111_L1.1730.97
94_Q111_L1.1600.97
121_K133_S1.1590.97
135_E144_I1.1490.97
70_M112_V1.1420.97
52_V58_R1.1210.96
95_L103_V1.1030.96
12_K30_Q1.1030.96
102_E132_R1.0980.96
41_F45_E1.0830.96
71_L81_S1.0770.95
16_S24_S1.0560.95
66_L95_L1.0550.95
10_D33_V1.0450.95
76_K125_I1.0410.94
11_T32_L1.0250.94
66_L108_I1.0200.94
18_L25_V1.0200.94
68_S72_R1.0190.94
106_K110_N0.9930.93
15_D120_D0.9900.93
69_G72_R0.9780.92
63_E67_R0.9720.92
138_K141_G0.9710.92
74_L88_I0.9710.92
111_L115_Q0.9660.92
15_D77_R0.9660.92
129_S140_F0.9660.92
113_M136_D0.9610.92
77_R129_S0.9550.91
107_M111_L0.9500.91
55_N69_G0.9450.91
18_L49_P0.9330.91
74_L84_V0.9310.90
73_A95_L0.9250.90
113_M135_E0.9220.90
135_E139_E0.9140.90
45_E101_R0.9110.89
11_T25_V0.9050.89
56_D79_V0.9010.89
67_R85_E0.8980.89
2_H7_F0.8870.88
122_V140_F0.8830.88
63_E88_I0.8790.88
11_T20_G0.8540.86
140_F144_I0.8540.86
115_Q118_K0.8530.86
43_V92_K0.8520.86
61_F92_K0.8460.86
125_I132_R0.8440.86
57_V79_V0.8410.85
61_F96_R0.8380.85
59_E69_G0.8260.84
58_R113_M0.8220.84
125_I138_K0.8210.84
70_M91_I0.8120.83
79_V119_L0.8090.83
51_V95_L0.8030.83
21_E98_T0.7990.82
110_N113_M0.7960.82
121_K144_I0.7960.82
50_R81_S0.7940.82
12_K143_E0.7940.82
30_Q105_S0.7890.81
11_T30_Q0.7880.81
2_H9_V0.7830.81
11_T18_L0.7740.80
91_I112_V0.7730.80
54_S63_E0.7660.80
20_G139_E0.7620.79
64_E93_S0.7580.79
3_C6_C0.7500.78
138_K145_A0.7400.77
102_E108_I0.7370.77
51_V61_F0.7310.76
49_P105_S0.7300.76
98_T103_V0.7250.76
86_M90_H0.7240.76
49_P95_L0.7220.75
9_V86_M0.7130.74
35_N55_N0.7110.74
139_E143_E0.6980.73
58_R76_K0.6980.73
128_A131_Y0.6970.73
121_K125_I0.6920.72
49_P96_R0.6900.72
11_T22_G0.6880.72
66_L70_M0.6850.72
48_M71_L0.6850.72
18_L139_E0.6800.71
61_F139_E0.6740.70
43_V72_R0.6740.70
32_L144_I0.6670.69
136_D139_E0.6660.69
47_V93_S0.6630.69
79_V101_R0.6620.69
31_C34_C0.6600.69
5_F11_T0.6540.68
113_M128_A0.6540.68
33_V123_A0.6530.68
89_N93_S0.6510.68
125_I144_I0.6480.67
61_F111_L0.6440.67
67_R71_L0.6420.67
91_I115_Q0.6390.66
59_E146_R0.6330.65
61_F106_K0.6310.65
1_M6_C0.6300.65
74_L92_K0.6240.64
15_D131_Y0.6240.64
63_E85_E0.6200.64
2_H18_L0.6190.64
69_G143_E0.6180.64
78_P120_D0.6180.64
60_P146_R0.6170.63
33_V106_K0.6160.63
113_M125_I0.6130.63
93_S100_E0.6100.63
64_E67_R0.6070.62
50_R57_V0.6060.62
5_F62_N0.6060.62
67_R70_M0.6040.62
122_V125_I0.5990.61
2_H46_L0.5900.60
52_V103_V0.5900.60
19_V41_F0.5880.60
79_V83_D0.5870.60
109_G130_V0.5820.59
85_E89_N0.5810.59
5_F9_V0.5740.58
1_M13_V0.5710.58
51_V107_M0.5710.58
63_E74_L0.5680.57
74_L122_V0.5650.57
44_A85_E0.5640.57
132_R135_E0.5600.56
73_A141_G0.5600.56
92_K96_R0.5600.56
131_Y140_F0.5570.56
81_S85_E0.5570.56
59_E75_E0.5550.55
20_G24_S0.5510.55
76_K88_I0.5500.55
69_G109_G0.5490.55
20_G43_V0.5460.54
14_I133_S0.5440.54
39_T114_E0.5430.54
45_E58_R0.5420.54
39_T89_N0.5410.54
110_N136_D0.5400.53
33_V104_P0.5390.53
114_E118_K0.5380.53
117_K121_K0.5380.53
90_H94_Q0.5380.53
78_P84_V0.5380.53
56_D59_E0.5340.53
127_F140_F0.5330.53
16_S113_M0.5250.51
11_T38_F0.5240.51
20_G23_S0.5200.51
62_N94_Q0.5170.50
7_F97_A0.5120.50
6_C13_V0.5120.50
47_V96_R0.5100.49
61_F141_G0.5090.49
45_E52_V0.5090.49
30_Q104_P0.5090.49
46_L96_R0.5090.49
15_D113_M0.5080.49
45_E82_D0.5080.49
32_L41_F0.5050.49
85_E102_E0.5050.49
22_G73_A0.5050.49
5_F100_E0.5010.48
75_E133_S0.5010.48
134_F140_F0.5000.48
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  
3ga8A 1 0.4094 98.1 0.863 Contact Map
1tfiA 1 0.2617 97.9 0.869 Contact Map
3k8tA 2 0.1208 97.6 0.876 Contact Map
3hncA 2 0.651 97.5 0.878 Contact Map
2xapA 4 0.6309 97.4 0.881 Contact Map
3o9xA 2 0.7852 95.4 0.905 Contact Map
1qypA 1 0.2685 91.8 0.918 Contact Map
1twfI 1 0.3221 90.7 0.92 Contact Map
3h0gI 1 0.2617 90.2 0.921 Contact Map
4c2mI 1 0.2819 89.9 0.922 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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