GREMLIN Database
RPOE - DNA-directed RNA polymerase subunit delta
UniProt: P12464 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 173 (168)
Sequences: 408 (326)
Seq/√Len: 25.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
124_D130_E3.7971.00
47_K50_E3.2401.00
16_L85_D3.1971.00
102_A105_A2.8010.99
37_L55_I2.6810.99
160_E168_E2.4060.98
58_F87_L2.3920.98
152_E155_E2.3720.98
7_S10_E2.3270.98
27_H39_E2.2660.98
44_L79_R2.2280.97
118_I121_D2.2200.97
133_D152_E2.1520.97
99_K102_A2.1140.96
71_L82_Y2.0580.96
40_I58_F2.0130.95
96_K99_K1.8830.93
110_L134_L1.7460.90
125_L128_V1.7280.90
31_V36_L1.7000.89
75_T90_E1.6960.89
31_V35_E1.6950.89
146_E154_E1.6930.89
14_M19_I1.6350.87
97_A102_A1.6270.87
112_L115_F1.6230.86
127_E137_D1.6170.86
163_E166_D1.6120.86
107_E110_L1.6100.86
135_E169_E1.5920.85
101_K104_K1.5720.85
113_D119_D1.5550.84
54_R79_R1.5260.83
49_E53_D1.5050.82
26_E29_K1.5010.82
127_E130_E1.4940.81
115_F120_E1.4870.81
41_A48_K1.4680.80
149_D156_D1.4210.78
145_D149_D1.4190.78
86_Q90_E1.4100.77
123_L132_L1.4080.77
19_I44_L1.4050.77
44_L58_F1.3990.77
31_V58_F1.3760.76
137_D140_D1.3520.74
13_E36_L1.3380.73
50_E89_E1.3370.73
30_P86_Q1.3340.73
77_G82_Y1.3250.73
8_Q88_D1.3090.72
64_I77_G1.3030.71
15_A18_E1.2950.71
58_F61_D1.2880.71
46_V51_L1.2860.70
27_H73_D1.2710.69
122_D147_D1.2640.69
69_L79_R1.2580.69
132_L144_L1.2550.68
21_H25_E1.2380.67
52_G91_T1.2350.67
25_E90_E1.2340.67
149_D155_E1.2310.67
24_F84_Y1.2220.66
111_D135_E1.2110.66
118_I123_L1.2110.66
120_E123_L1.2050.65
11_L86_Q1.1770.63
73_D79_R1.1720.63
157_I160_E1.1640.63
19_I73_D1.1520.62
32_P35_E1.1390.61
152_E157_I1.1360.61
100_K103_K1.1330.60
36_L45_G1.1270.60
120_E130_E1.1250.60
39_E42_S1.1200.59
37_L40_I1.1090.59
37_L79_R1.1060.58
50_E55_I1.0870.57
49_E125_L1.0690.56
99_K103_K1.0620.55
118_I141_E1.0590.55
29_K75_T1.0560.55
127_E132_L1.0490.54
40_I128_V1.0470.54
145_D148_D1.0360.53
19_I43_L1.0250.53
21_H28_K1.0230.53
11_L14_M1.0080.51
38_N42_S1.0030.51
35_E52_G1.0010.51
45_G55_I1.0000.51
135_E164_D0.9940.50
109_D117_E0.9760.49
97_A104_K0.9700.49
6_Y73_D0.9690.49
156_D165_Y0.9590.48
37_L94_T0.9570.48
54_R84_Y0.9480.47
122_D125_L0.9460.47
27_H51_L0.9440.47
117_E122_D0.9340.46
9_E89_E0.9300.46
71_L77_G0.9260.45
97_A101_K0.9240.45
113_D124_D0.9220.45
141_E144_L0.9210.45
57_Q61_D0.9140.45
133_D136_A0.9010.44
109_D112_L0.8970.43
37_L51_L0.8890.43
42_S153_I0.8880.43
27_H42_S0.8870.43
163_E169_E0.8870.43
35_E108_E0.8870.43
110_L144_L0.8860.43
44_L88_D0.8850.43
11_L43_L0.8800.42
113_D116_E0.8800.42
3_I97_A0.8690.41
24_F56_A0.8690.41
138_D143_D0.8690.41
92_Q98_K0.8580.41
164_D168_E0.8570.41
86_Q102_A0.8550.40
6_Y118_I0.8520.40
9_E117_E0.8510.40
37_L44_L0.8380.39
115_F118_I0.8310.39
132_L142_E0.8260.38
87_L93_P0.8260.38
71_L75_T0.8160.38
61_D69_L0.8150.38
126_D129_E0.8130.38
33_F69_L0.8000.37
111_D121_D0.8000.37
122_D132_L0.7970.36
70_A91_T0.7960.36
110_L117_E0.7890.36
38_N51_L0.7820.35
33_F41_A0.7810.35
7_S93_P0.7800.35
6_Y9_E0.7780.35
71_L89_E0.7750.35
98_K101_K0.7720.35
43_L67_R0.7610.34
153_I158_I0.7580.34
87_L91_T0.7480.33
16_L80_S0.7440.33
2_G28_K0.7410.33
27_H79_R0.7400.33
41_A79_R0.7350.32
129_E147_D0.7310.32
150_D154_E0.7300.32
145_D166_D0.7240.32
130_E151_L0.7220.32
138_D144_L0.7160.31
157_I167_D0.7020.30
133_D144_L0.6980.30
127_E139_F0.6970.30
117_E142_E0.6930.30
18_E80_S0.6900.30
80_S98_K0.6890.30
64_I93_P0.6850.29
3_I23_L0.6840.29
32_P97_A0.6810.29
131_E167_D0.6800.29
57_Q94_T0.6750.29
149_D152_E0.6730.29
10_E86_Q0.6700.28
6_Y43_L0.6680.28
117_E127_E0.6630.28
48_K103_K0.6550.27
34_Q54_R0.6530.27
57_Q60_T0.6510.27
37_L73_D0.6460.27
24_F57_Q0.6420.27
143_D147_D0.6360.26
18_E115_F0.6340.26
142_E164_D0.6290.26
33_F58_F0.6280.26
5_Q77_G0.6280.26
16_L30_P0.6270.26
124_D129_E0.6200.26
140_D169_E0.6190.25
126_D167_D0.6150.25
10_E90_E0.6130.25
134_L145_D0.6110.25
135_E163_E0.6100.25
164_D167_D0.5990.24
36_L62_L0.5990.24
35_E93_P0.5950.24
136_A148_D0.5930.24
148_D157_I0.5930.24
147_D152_E0.5900.24
150_D167_D0.5890.24
97_A112_L0.5890.24
23_L153_I0.5860.24
16_L84_Y0.5850.24
59_Y66_G0.5830.24
123_L126_D0.5820.23
147_D159_D0.5820.23
30_P77_G0.5800.23
17_V70_A0.5720.23
10_E93_P0.5700.23
128_V168_E0.5670.23
155_E159_D0.5660.23
61_D93_P0.5660.23
75_T87_L0.5660.23
33_F40_I0.5630.22
109_D148_D0.5600.22
28_K79_R0.5600.22
70_A86_Q0.5600.22
130_E149_D0.5590.22
96_K100_K0.5590.22
4_K7_S0.5540.22
39_E64_I0.5520.22
69_L87_L0.5520.22
137_D156_D0.5490.22
141_E159_D0.5470.22
159_D167_D0.5470.22
106_V160_E0.5450.22
153_I160_E0.5450.22
19_I70_A0.5420.21
50_E110_L0.5410.21
22_E92_Q0.5400.21
42_S116_E0.5390.21
108_E138_D0.5390.21
48_K155_E0.5390.21
2_G5_Q0.5370.21
11_L88_D0.5360.21
3_I59_Y0.5360.21
23_L71_L0.5350.21
30_P87_L0.5340.21
56_A80_S0.5340.21
39_E82_Y0.5310.21
24_F81_W0.5290.21
31_V62_L0.5260.21
14_M33_F0.5260.21
19_I40_I0.5250.21
53_D129_E0.5220.20
62_L67_R0.5190.20
133_D168_E0.5190.20
8_Q11_L0.5180.20
153_I157_I0.5160.20
131_E137_D0.5120.20
11_L67_R0.5110.20
140_D168_E0.5110.20
33_F72_S0.5090.20
21_H73_D0.5000.19
73_D95_V0.5000.19
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  
2krcA 1 0.5723 100 0.397 Contact Map
4u7aA 1 0 97.4 0.869 Contact Map
4fp9B 2 0.6185 89 0.914 Contact Map
4fdgB 1 0.0116 53.5 0.937 Contact Map
3q9sA 1 0.3931 36.9 0.943 Contact Map
1wj7A 1 0.5376 36.6 0.943 Contact Map
3go5A 1 0.3815 29.7 0.946 Contact Map
4bjqA 2 0.422 28.3 0.946 Contact Map
2ma3A 1 0.4277 28.1 0.946 Contact Map
3h93A 1 0.6012 24.9 0.948 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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