GREMLIN Database
RFAH - Transcription antitermination protein RfaH
UniProt: P0AFW0 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10839
Length: 162 (159)
Sequences: 2861 (1625)
Seq/√Len: 128.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
18_Q22_E5.1901.00
139_S159_F4.2601.00
27_N58_E4.1541.00
34_T45_A3.9321.00
90_S94_H3.8351.00
117_I160_R3.0511.00
34_T47_S2.7891.00
132_E140_M2.5681.00
138_R153_S2.5381.00
115_K127_Q2.1651.00
114_D161_K2.1281.00
26_V58_E2.1181.00
37_K48_E2.1131.00
32_M47_S2.0201.00
120_E158_E1.9871.00
141_L154_V1.9091.00
62_E65_H1.9071.00
24_Q72_T1.7821.00
13_Q74_G1.7131.00
36_E45_A1.6941.00
38_I43_R1.6881.00
117_I127_Q1.6431.00
17_A75_V1.6381.00
15_Q32_M1.6121.00
131_T142_L1.5791.00
29_L100_K1.5571.00
134_D137_A1.5551.00
59_F65_H1.5471.00
7_L75_V1.5381.00
51_F56_F1.5341.00
21_L69_I1.4961.00
8_Y76_S1.4791.00
128_A141_L1.4461.00
70_N77_H1.4461.00
36_E43_R1.4421.00
88_V93_I1.4371.00
91_A94_H1.4261.00
130_F133_P1.4181.00
144_N149_E1.4151.00
135_G156_N1.4061.00
138_R155_K1.4051.00
9_C14_L1.4031.00
33_I48_E1.4021.00
116_V141_L1.3861.00
59_F69_I1.3761.00
142_L149_E1.3591.00
117_I125_G1.3301.00
27_N97_S1.2991.00
154_V158_E1.2831.00
56_F96_L1.2581.00
39_V44_T1.2541.00
93_I97_S1.2511.00
19_E23_R1.2471.00
16_R19_E1.2461.00
35_L48_E1.2461.00
51_F96_L1.2331.00
111_Y114_D1.2271.00
119_T160_R1.2180.99
142_L151_K1.2150.99
21_L75_V1.2110.99
6_L88_V1.1870.99
155_K158_E1.1860.99
67_T71_A1.1630.99
7_L57_V1.1610.99
118_I154_V1.1600.99
24_Q73_R1.1550.99
3_S87_I1.1230.99
73_R96_L1.1190.99
99_Y106_D1.1180.99
112_P133_P1.0980.99
140_M151_K1.0770.99
10_K13_Q1.0740.99
3_S90_S1.0690.99
63_V84_S1.0690.99
10_K74_G1.0650.99
50_L56_F1.0620.99
8_Y77_H1.0570.99
58_E90_S1.0510.98
154_V159_F1.0310.98
65_H69_I1.0280.98
146_I150_I1.0220.98
13_Q16_R1.0190.98
96_L100_K1.0050.98
134_D153_S1.0050.98
8_Y53_N1.0050.98
139_S156_N0.9940.98
18_Q30_A0.9860.98
131_T151_K0.9730.98
116_V128_A0.9700.97
29_L97_S0.9510.97
9_C13_Q0.9490.97
91_A95_Q0.9140.96
59_F66_T0.9090.96
22_E28_C0.9070.96
7_L69_I0.8940.96
38_I157_T0.8910.96
16_R74_G0.8810.96
17_A72_T0.8800.96
138_R146_I0.8710.95
110_P130_F0.8580.95
20_H24_Q0.8570.95
39_V42_K0.8390.94
81_F86_A0.8300.94
141_L159_F0.8230.94
115_K129_I0.8160.93
52_P69_I0.8090.93
103_D106_D0.8060.93
110_P114_D0.8010.93
117_I126_F0.7980.93
111_Y161_K0.7880.92
80_R83_A0.7880.92
89_P92_V0.7790.92
26_V60_D0.7760.91
66_T70_N0.7750.91
16_R20_H0.7740.91
112_P139_S0.7690.91
13_Q20_H0.7680.91
14_L30_A0.7670.91
25_A28_C0.7630.91
6_L79_V0.7570.90
140_M147_N0.7570.90
126_F146_I0.7550.90
20_H72_T0.7510.90
112_P132_E0.7500.90
17_A20_H0.7490.90
94_H98_V0.7420.90
28_C31_P0.7390.89
14_L54_Y0.7340.89
80_R87_I0.7310.89
76_S80_R0.7290.89
140_M153_S0.7160.88
11_R14_L0.7090.87
24_Q68_T0.7080.87
30_A55_L0.7070.87
11_R17_A0.7030.87
26_V40_R0.6950.86
118_I147_N0.6910.86
77_H80_R0.6870.86
23_R74_G0.6860.86
147_N150_I0.6860.86
66_T85_P0.6760.85
29_L51_F0.6760.85
7_L23_R0.6750.85
15_Q19_E0.6740.85
24_Q71_A0.6690.84
128_A152_H0.6680.84
143_L151_K0.6660.84
21_L72_T0.6650.84
31_P55_L0.6630.84
89_P97_S0.6620.84
30_A49_P0.6610.83
17_A21_L0.6590.83
88_V144_N0.6560.83
29_L96_L0.6550.83
143_L150_I0.6550.83
95_Q99_Y0.6550.83
81_F84_S0.6520.83
6_L74_G0.6470.82
134_D138_R0.6410.82
61_P66_T0.6390.81
99_Y125_G0.6370.81
79_V135_G0.6330.81
20_H89_P0.6320.81
133_P139_S0.6320.81
17_A92_V0.6310.81
59_F80_R0.6260.80
122_A126_F0.6240.80
106_D135_G0.6220.80
95_Q98_V0.6210.79
35_L145_L0.6120.78
130_F159_F0.6110.78
15_Q49_P0.6110.78
17_A55_L0.6110.78
141_L147_N0.6100.78
9_C53_N0.6070.78
25_A69_I0.6000.77
16_R72_T0.5970.77
126_F141_L0.5960.77
19_E22_E0.5920.76
65_H68_T0.5920.76
131_T140_M0.5900.76
89_P94_H0.5890.76
58_E101_P0.5870.76
12_G30_A0.5850.75
137_A155_K0.5830.75
79_V83_A0.5820.75
75_V123_F0.5800.75
38_I41_G0.5770.74
144_N154_V0.5770.74
141_L151_K0.5670.73
68_T71_A0.5670.73
126_F150_I0.5640.73
73_R81_F0.5610.72
110_P159_F0.5600.72
8_Y13_Q0.5580.72
38_I42_K0.5580.72
12_G139_S0.5580.72
56_F88_V0.5520.71
57_V65_H0.5500.71
9_C119_T0.5500.71
67_T70_N0.5490.71
126_F143_L0.5470.70
21_L24_Q0.5460.70
108_A156_N0.5450.70
70_N74_G0.5420.70
90_S96_L0.5400.69
86_A92_V0.5390.69
135_G142_L0.5380.69
34_T91_A0.5320.68
58_E97_S0.5310.68
30_A56_F0.5290.68
113_G136_E0.5290.68
29_L56_F0.5290.68
131_T141_L0.5260.67
49_P83_A0.5250.67
23_R81_F0.5240.67
98_V101_P0.5220.67
12_G17_A0.5220.67
111_Y116_V0.5200.67
53_N100_K0.5190.66
11_R16_R0.5190.66
63_V66_T0.5180.66
58_E89_P0.5170.66
29_L34_T0.5160.66
125_G152_H0.5150.66
44_T48_E0.5150.66
127_Q160_R0.5140.66
79_V97_S0.5130.65
75_V85_P0.5130.65
107_P111_Y0.5120.65
9_C79_V0.5110.65
106_D144_N0.5090.65
113_G129_I0.5080.65
122_A140_M0.5060.64
20_H73_R0.5060.64
40_R44_T0.5040.64
98_V103_D0.5010.64
5_Y14_L0.5000.64
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  
2ougA 1 0.8642 100 0.109 Contact Map
2jvvA 1 0.358 100 0.147 Contact Map
1m1hA 1 0.6296 100 0.168 Contact Map
2lq8A 1 0.9568 100 0.19 Contact Map
2xhcA 1 0.9506 100 0.275 Contact Map
3p8bB 2 0.8765 100 0.314 Contact Map
1nz8A 1 0.642 99.9 0.454 Contact Map
3lpeA 1 0.5123 99.8 0.597 Contact Map
2mi6A 1 0.3765 99.4 0.699 Contact Map
2e6zA 1 0.3642 99.4 0.703 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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