GREMLIN Database
RPOD - DNA-directed RNA polymerase subunit D
UniProt: Q9HQJ4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 248 (240)
Sequences: 814 (556)
Seq/√Len: 35.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
70_V117_I6.6201.00
37_I227_L5.6461.00
91_E125_R4.3531.00
216_V228_V3.8301.00
95_T116_P3.3321.00
79_A82_E3.3161.00
192_N195_T3.2891.00
101_L130_A3.2051.00
89_D127_E3.1971.00
56_S120_L3.1341.00
195_T198_Y3.1331.00
72_L132_A3.0921.00
52_V127_E2.9381.00
139_D143_H2.9281.00
58_M118_I2.7591.00
89_D125_R2.4741.00
78_Y82_E2.4671.00
103_S107_E2.4381.00
230_R233_D2.4371.00
76_E79_A2.4231.00
46_I67_L2.4091.00
173_M178_I2.2530.99
37_I216_V2.2320.99
173_M195_T2.2010.99
174_L178_I2.1980.99
170_D174_L2.1800.99
20_F30_A2.1450.99
170_D173_M2.1380.99
33_I228_V2.1360.99
192_N198_Y2.1000.99
53_E125_R2.0500.99
188_D191_D2.0290.99
49_V67_L2.0090.98
173_M192_N1.9720.98
218_S227_L1.8850.98
76_E82_E1.8690.97
50_R131_D1.8650.97
85_T129_E1.8420.97
10_F18_A1.8120.97
31_N34_R1.7790.97
51_F128_L1.7380.96
174_L192_N1.6160.94
13_R18_A1.6080.94
13_R225_E1.5990.94
51_F64_G1.5880.94
56_S118_I1.5880.94
166_Y173_M1.5760.93
21_V190_F1.5370.92
53_E127_E1.5360.92
160_V204_E1.5010.91
104_N107_E1.4870.91
12_D19_R1.4800.91
23_R211_A1.4540.90
166_Y169_D1.4220.89
6_F22_V1.4020.88
22_V25_I1.4010.88
176_G187_T1.4000.88
169_D174_L1.3860.88
74_T84_V1.3800.88
171_P174_L1.3750.87
98_S115_I1.3530.87
86_L98_S1.3510.86
25_I29_F1.3420.86
118_I126_L1.3310.86
197_R200_G1.3280.85
92_G121_K1.3220.85
26_T212_F1.2840.83
195_T199_P1.2650.83
135_G139_D1.2600.82
166_Y174_L1.2530.82
165_E197_R1.2490.82
44_L74_T1.2440.81
40_D238_R1.2350.81
27_P151_Y1.2260.80
22_V30_A1.2230.80
101_L224_V1.2040.79
137_G145_G1.1980.79
92_G212_F1.1880.78
173_M198_Y1.1830.78
43_T219_D1.1800.78
9_E22_V1.1690.77
40_D136_H1.1540.76
10_F224_V1.1460.76
75_P234_T1.1390.75
38_L144_Q1.1380.75
101_L124_Q1.1380.75
44_L222_M1.1340.75
173_M177_V1.1200.74
192_N199_P1.1190.74
88_L128_L1.0940.72
26_T36_A1.0850.72
86_L103_S1.0790.71
58_M63_L1.0790.71
24_N210_G1.0690.71
170_D192_N1.0570.70
58_M222_M1.0380.68
31_N35_R1.0320.68
99_G114_N1.0310.68
102_V105_D1.0300.68
40_D234_T1.0250.67
199_P205_I1.0250.67
174_L177_V1.0210.67
36_A40_D1.0090.66
95_T159_V1.0030.66
111_A132_A1.0030.66
170_D178_I1.0010.65
48_T131_D0.9840.64
174_L195_T0.9750.63
217_E220_G0.9720.63
77_D96_A0.9710.63
117_I231_A0.9690.63
168_D172_Q0.9400.60
47_D133_V0.9290.60
193_D196_T0.9220.59
175_R178_I0.9210.59
166_Y170_D0.9200.59
174_L198_Y0.9200.59
156_R206_E0.9200.59
170_D201_K0.9150.58
46_I49_V0.9120.58
11_V21_V0.9100.58
234_T238_R0.9040.57
30_A37_I0.9010.57
15_D224_V0.8980.57
8_V104_N0.8960.57
80_A85_T0.8950.57
158_H204_E0.8910.56
59_F62_Q0.8860.56
17_E215_H0.8830.56
237_D241_E0.8820.56
20_F214_F0.8750.55
170_D195_T0.8740.55
159_V165_E0.8670.54
165_E173_M0.8660.54
18_A181_D0.8650.54
16_R246_V0.8560.53
232_V236_V0.8510.53
72_L84_V0.8500.53
6_F25_I0.8410.52
160_V163_S0.8410.52
58_M77_D0.8340.51
109_E113_E0.8260.51
176_G188_D0.8260.51
224_V238_R0.8240.50
166_Y195_T0.8210.50
100_D120_L0.8120.49
58_M62_Q0.8090.49
97_Y100_D0.8090.49
101_L181_D0.8060.49
53_E63_L0.8030.49
21_V211_A0.8000.48
171_P176_G0.7920.48
57_V89_D0.7900.48
163_S184_L0.7890.47
86_L101_L0.7870.47
72_L85_T0.7870.47
87_A127_E0.7860.47
37_I146_G0.7850.47
150_G215_H0.7800.47
46_I132_A0.7700.46
46_I62_Q0.7660.45
44_L67_L0.7650.45
10_F76_E0.7640.45
170_D175_R0.7610.45
108_V128_L0.7550.45
36_A235_L0.7540.44
184_L239_A0.7480.44
28_A181_D0.7460.44
22_V33_I0.7420.43
10_F24_N0.7420.43
89_D242_L0.7420.43
215_H228_V0.7400.43
127_E215_H0.7390.43
164_P182_D0.7360.43
44_L226_E0.7360.43
10_F13_R0.7320.43
119_E143_H0.7300.42
228_V231_A0.7230.42
104_N109_E0.7210.42
166_Y194_L0.7190.41
103_S106_P0.7140.41
93_P121_K0.7110.41
157_V170_D0.7110.41
171_P175_R0.7100.41
46_I134_M0.7090.41
81_G242_L0.7070.40
24_N63_L0.7060.40
193_D198_Y0.6990.40
63_L218_S0.6970.40
52_V101_L0.6950.39
195_T201_K0.6940.39
41_V183_E0.6940.39
173_M201_K0.6920.39
215_H218_S0.6900.39
12_D16_R0.6890.39
139_D154_L0.6890.39
63_L84_V0.6880.39
20_F228_V0.6880.39
173_M176_G0.6870.39
161_G204_E0.6870.39
43_T54_N0.6840.39
154_L211_A0.6830.38
72_L133_V0.6830.38
56_S126_L0.6770.38
27_P227_L0.6750.38
8_V123_D0.6750.38
44_L113_E0.6740.38
39_V43_T0.6740.38
116_P119_E0.6730.38
156_R223_P0.6650.37
57_V235_L0.6640.37
114_N216_V0.6600.37
90_V94_G0.6600.37
222_M230_R0.6600.37
18_A225_E0.6570.36
70_V213_V0.6560.36
236_V240_D0.6560.36
72_L97_Y0.6550.36
169_D173_M0.6530.36
89_D130_A0.6500.36
101_L110_A0.6480.36
190_F194_L0.6480.36
40_D56_S0.6470.36
29_F219_D0.6430.35
25_I33_I0.6410.35
67_L77_D0.6410.35
135_G143_H0.6400.35
71_P115_I0.6380.35
99_G113_E0.6370.35
98_S113_E0.6350.35
153_H157_V0.6350.35
178_I192_N0.6340.35
81_G111_A0.6310.34
18_A224_V0.6280.34
142_K145_G0.6240.34
154_L208_V0.6230.34
40_D120_L0.6230.34
214_F217_E0.6220.34
14_D18_A0.6200.33
157_V196_T0.6180.33
9_E114_N0.6150.33
152_R207_D0.6150.33
134_M230_R0.6140.33
114_N122_D0.6140.33
74_T108_V0.6130.33
9_E216_V0.6110.33
72_L240_D0.6100.33
215_H227_L0.6080.33
165_E201_K0.6080.33
5_D24_N0.6070.32
159_V163_S0.6060.32
191_D198_Y0.6050.32
152_R157_V0.6040.32
156_R208_V0.6040.32
226_E230_R0.6030.32
74_T151_Y0.6030.32
223_P227_L0.6020.32
25_I62_Q0.6010.32
18_A231_A0.5980.32
67_L76_E0.5950.32
106_P176_G0.5920.31
120_L168_D0.5920.31
20_F216_V0.5920.31
7_D24_N0.5920.31
127_E130_A0.5910.31
43_T124_Q0.5900.31
47_D131_D0.5890.31
14_D222_M0.5890.31
46_I147_V0.5880.31
36_A234_T0.5850.31
167_A171_P0.5850.31
196_T200_G0.5840.31
57_V132_A0.5830.31
193_D199_P0.5820.31
106_P134_M0.5760.30
61_E66_R0.5750.30
67_L117_I0.5750.30
32_G62_Q0.5750.30
25_I241_E0.5740.30
146_G219_D0.5730.30
50_R129_E0.5730.30
146_G149_V0.5720.30
182_D185_V0.5710.30
194_L197_R0.5710.30
225_E229_L0.5710.30
12_D102_V0.5700.30
103_S110_A0.5700.30
62_Q122_D0.5700.30
33_I232_V0.5680.30
146_G227_L0.5680.30
117_I156_R0.5670.29
176_G185_V0.5660.29
28_A139_D0.5660.29
30_A34_R0.5650.29
149_V153_H0.5620.29
54_N88_L0.5620.29
77_D97_Y0.5610.29
87_A129_E0.5590.29
154_L213_V0.5580.29
14_D17_E0.5580.29
97_Y116_P0.5580.29
83_A131_D0.5570.29
56_S127_E0.5570.29
137_G144_Q0.5570.29
151_Y214_F0.5570.29
64_G85_T0.5560.29
41_V59_F0.5560.29
196_T199_P0.5550.29
43_T134_M0.5550.29
47_D142_K0.5550.29
37_I147_V0.5520.28
43_T69_L0.5520.28
8_V20_F0.5520.28
167_A175_R0.5500.28
32_G147_V0.5470.28
9_E21_V0.5460.28
172_Q237_D0.5460.28
75_P223_P0.5450.28
101_L242_L0.5450.28
77_D113_E0.5450.28
167_A170_D0.5430.28
37_I141_A0.5420.28
197_R201_K0.5420.28
69_L102_V0.5390.27
155_Q238_R0.5380.27
130_A169_D0.5380.27
82_E85_T0.5370.27
47_D151_Y0.5340.27
33_I240_D0.5340.27
169_D192_N0.5330.27
169_D175_R0.5320.27
74_T224_V0.5310.27
119_E212_F0.5300.27
51_F214_F0.5300.27
166_Y192_N0.5300.27
43_T62_Q0.5280.27
44_L80_A0.5280.27
160_V206_E0.5270.27
73_T109_E0.5260.27
229_L233_D0.5250.27
44_L48_T0.5250.27
90_V184_L0.5240.26
19_R191_D0.5230.26
130_A158_H0.5210.26
158_H206_E0.5190.26
80_A150_G0.5170.26
140_H145_G0.5150.26
98_S227_L0.5140.26
171_P191_D0.5130.26
113_E164_P0.5130.26
171_P192_N0.5090.25
89_D126_L0.5090.25
190_F198_Y0.5090.25
20_F25_I0.5070.25
109_E132_A0.5060.25
30_A185_V0.5040.25
243_E246_V0.5030.25
222_M227_L0.5010.25
88_L117_I0.5000.25
56_S157_V0.5000.25
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  
4c2mC 1 1 100 0.253 Contact Map
2pa8D 1 0.9637 100 0.289 Contact Map
4qjvA 1 0.9798 100 0.308 Contact Map
3h0gC 1 0.9315 100 0.346 Contact Map
1twfC 1 0.9395 100 0.348 Contact Map
2a6hA 2 0.8347 100 0.507 Contact Map
4noiA 2 0.8306 100 0.51 Contact Map
1bdfA 4 0.8387 100 0.523 Contact Map
4yfkA 2 0.8589 100 0.524 Contact Map
2pa8L 1 0.3589 95 0.931 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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