GREMLIN Database
RPOD - DNA-directed RNA polymerase subunit D
UniProt: P95989 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 265 (255)
Sequences: 810 (559)
Seq/√Len: 35.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
65_I130_I6.7711.00
32_S241_I5.9671.00
101_E138_K4.5801.00
203_C206_C3.8881.00
230_I242_L3.7411.00
108_M129_P3.7331.00
67_F145_L3.4651.00
89_C92_C3.3991.00
99_E140_S3.3711.00
183_C203_C3.2741.00
114_I143_A3.1811.00
152_E156_F3.0691.00
51_S133_L3.0241.00
82_C92_C3.0201.00
183_C206_C2.9511.00
47_I140_S2.8901.00
53_L131_V2.8231.00
199_N202_S2.8151.00
206_C209_C2.7651.00
99_E138_K2.6801.00
244_E247_K2.6111.00
82_C89_C2.5761.00
41_V62_L2.5051.00
116_S120_S2.4221.00
97_Y115_K2.3350.99
183_C209_C2.2650.99
15_L25_V2.2360.99
48_E138_K2.1210.99
32_S230_I2.0990.99
232_S241_I2.0830.99
203_C209_C1.9900.98
5_L13_I1.9660.98
39_M74_D1.9630.98
44_V62_L1.9560.98
28_I242_L1.9520.98
117_E120_S1.9260.98
26_N29_R1.8340.97
51_S131_V1.8160.97
46_F141_L1.7520.96
45_Y144_R1.7490.96
39_M76_Y1.7170.95
95_K142_E1.7020.95
46_F59_A1.6910.95
176_C195_L1.6750.95
16_V201_L1.6500.94
180_V188_F1.6450.94
189_E198_K1.6380.94
173_L218_R1.6100.94
183_C188_F1.6050.93
184_P209_C1.5810.93
48_E140_S1.5720.93
177_E193_G1.5720.93
35_Y252_K1.5710.93
17_F20_Y1.5340.92
98_I141_L1.5230.92
111_S128_I1.5190.91
189_E192_D1.4890.91
20_Y24_F1.4860.90
8_K239_E1.4460.89
72_A244_E1.3850.87
69_S94_T1.3780.87
131_V139_I1.3760.87
7_H14_D1.3440.85
102_A134_G1.3360.85
18_E225_K1.3200.84
88_N93_Y1.2980.83
189_E199_N1.2960.83
8_K13_I1.2940.83
70_E248_S1.2920.83
96_I111_S1.2850.83
174_A216_S1.2660.82
206_C210_L1.2630.82
188_F203_C1.2610.81
186_G206_C1.2520.81
21_P226_Y1.2460.81
78_W82_C1.2250.80
41_V44_V1.2200.79
189_E196_S1.2120.79
148_G152_E1.1980.78
38_I233_V1.1940.78
180_V184_P1.1870.77
33_M157_I1.1750.77
42_D146_R1.1690.76
184_P188_F1.1470.75
122_V126_G1.1460.75
184_P203_C1.1450.75
35_Y248_S1.1390.74
150_G158_P1.1360.74
5_L238_P1.1290.74
22_L164_V1.1170.73
102_A226_Y1.1090.72
184_P187_V1.0940.71
26_N30_R1.0740.70
54_Y57_I1.0650.69
19_G224_D1.0620.69
124_I145_L1.0590.69
25_V32_S1.0590.69
35_Y149_Y1.0580.69
191_K196_S1.0480.68
184_P206_C1.0470.68
17_F25_V1.0450.68
116_S119_P1.0340.67
171_E218_R1.0270.66
39_M69_S1.0180.66
251_R255_E1.0120.65
53_L236_L1.0000.64
208_E211_R0.9980.64
53_L58_L0.9900.63
210_L219_I0.9830.63
108_M172_I0.9830.63
112_K127_D0.9790.63
21_P31_A0.9790.63
183_C186_G0.9760.62
58_L232_S0.9660.61
39_M236_L0.9570.61
88_N95_K0.9540.61
248_S252_K0.9490.60
206_C212_Y0.9430.60
65_I227_I0.9400.59
204_T207_E0.9400.59
103_P134_G0.9220.58
4_N17_F0.9210.58
5_L8_K0.9190.58
177_E180_V0.9150.57
10_D238_P0.9150.57
114_I238_P0.9050.56
100_A107_R0.8990.56
169_K220_S0.8970.56
31_A35_Y0.8960.56
77_R81_E0.8940.55
195_L200_E0.8910.55
2_S94_T0.8860.55
43_D144_R0.8820.54
52_P99_E0.8800.54
180_V195_L0.8730.54
180_V190_L0.8720.54
110_Y113_D0.8700.53
229_E242_L0.8690.53
51_S139_I0.8680.53
90_E95_K0.8680.53
238_P252_K0.8650.53
15_L228_L0.8640.53
188_F197_V0.8590.53
183_C187_V0.8550.52
203_C207_E0.8540.52
118_D122_V0.8530.52
99_E256_L0.8410.51
97_Y140_S0.8410.51
178_K214_N0.8400.51
178_K208_E0.8400.51
163_V229_E0.8300.50
47_I114_I0.8240.50
33_M75_T0.8210.49
201_L209_C0.8210.49
143_A182_V0.8190.49
53_L57_I0.8170.49
132_L156_F0.8020.48
114_I137_Q0.7990.47
73_L244_E0.7940.47
166_Y170_V0.7900.47
242_L245_A0.7890.47
172_I179_A0.7890.47
167_Y222_V0.7870.46
187_V203_C0.7830.46
67_F95_K0.7780.46
76_Y150_G0.7780.46
20_Y28_I0.7760.45
229_E241_I0.7750.45
112_K126_G0.7720.45
188_F206_C0.7690.45
38_I64_L0.7660.45
41_V147_L0.7630.44
9_D236_L0.7630.44
48_E58_L0.7620.44
203_C210_L0.7560.44
150_G157_I0.7470.43
72_A240_R0.7410.42
231_E234_G0.7390.42
34_L38_I0.7370.42
4_N230_I0.7350.42
78_W81_E0.7310.42
130_I245_A0.7270.41
174_A218_R0.7260.41
32_S159_V0.7260.41
58_L94_T0.7240.41
246_G250_I0.7140.40
167_Y225_K0.7130.40
39_M240_R0.7130.40
79_P246_G0.7120.40
12_R229_E0.7110.40
67_F94_T0.7070.40
75_T91_K0.7060.40
198_K201_L0.7030.39
117_E122_V0.7020.39
252_K260_L0.7020.39
114_I123_P0.7000.39
16_V225_K0.6940.39
6_L256_L0.6890.38
169_K222_V0.6870.38
23_E39_M0.6870.38
67_F146_R0.6860.38
9_D12_R0.6860.38
178_K212_Y0.6840.38
41_V145_L0.6830.38
170_V180_V0.6820.38
28_I93_Y0.6800.37
49_N55_D0.6780.37
127_D230_I0.6730.37
93_Y144_R0.6720.37
22_L241_I0.6700.37
67_F82_C0.6680.36
185_E206_C0.6680.36
31_A249_I0.6670.36
250_I254_E0.6670.36
20_Y255_E0.6630.36
39_M126_G0.6630.36
24_F249_I0.6620.36
13_I60_H0.6620.36
114_I141_L0.6600.36
191_K194_K0.6570.36
27_A57_I0.6570.36
94_T138_K0.6560.36
96_I114_I0.6540.35
6_L16_V0.6540.35
119_P147_L0.6520.35
100_A112_K0.6510.35
156_F159_V0.6500.35
31_A248_S0.6480.35
165_R170_V0.6440.35
240_R244_E0.6430.35
52_P249_I0.6430.35
117_E121_V0.6390.34
198_K202_S0.6390.34
254_E257_E0.6390.34
116_S122_V0.6390.34
62_L130_I0.6360.34
111_S126_G0.6360.34
35_Y133_L0.6360.34
67_F254_E0.6340.34
96_I116_S0.6310.34
216_S220_S0.6310.34
140_S229_E0.6310.34
177_E190_L0.6300.34
195_L253_I0.6220.33
7_H11_T0.6220.33
36_V64_L0.6210.33
34_L50_N0.6210.33
38_I190_L0.6210.33
58_L209_C0.6190.33
20_Y57_I0.6160.32
41_V57_I0.6150.32
39_M62_L0.6140.32
25_V29_R0.6140.32
67_F213_C0.6140.32
38_I49_N0.6130.32
24_F33_M0.6110.32
38_I147_L0.6110.32
237_K241_I0.6100.32
159_V233_V0.6100.32
34_L222_V0.6100.32
230_I248_S0.6090.32
25_V147_L0.6080.32
168_P252_K0.6070.32
77_R80_E0.6060.32
193_G196_S0.6050.32
186_G203_C0.6040.32
19_G123_P0.6030.31
148_G156_F0.6030.31
13_I238_P0.6020.31
12_R18_E0.6000.31
165_R221_F0.5980.31
109_I133_L0.5970.31
118_D123_P0.5960.31
182_V188_F0.5960.31
121_V141_L0.5930.31
69_S235_S0.5860.30
186_G189_E0.5850.30
99_E143_A0.5840.30
66_P128_I0.5830.30
96_I143_A0.5820.30
57_I156_F0.5810.30
113_D133_L0.5800.30
173_L191_K0.5800.30
43_D146_R0.5790.30
52_P194_K0.5790.30
39_M160_S0.5790.30
14_D201_L0.5780.30
65_I123_P0.5770.30
11_T241_I0.5760.30
68_M181_N0.5730.29
24_F233_V0.5720.29
119_P122_V0.5720.29
228_L231_E0.5710.29
133_L181_N0.5710.29
110_Y129_P0.5700.29
111_S241_I0.5680.29
118_D121_V0.5670.29
95_K116_S0.5670.29
90_E163_V0.5630.29
189_E195_L0.5620.29
58_L141_L0.5610.28
127_D135_T0.5580.28
184_P204_T0.5580.28
36_V194_K0.5580.28
17_F28_I0.5580.28
180_V183_C0.5570.28
91_K124_I0.5550.28
17_F94_T0.5550.28
9_D91_K0.5550.28
163_V166_Y0.5540.28
203_C212_Y0.5530.28
4_N127_D0.5530.28
69_S238_P0.5520.28
243_L247_K0.5500.28
68_M122_V0.5490.28
104_N107_R0.5490.28
212_Y215_G0.5480.28
159_V241_I0.5480.28
21_P65_I0.5480.28
36_V112_K0.5460.27
98_I123_P0.5460.27
159_V162_S0.5450.27
61_R153_H0.5430.27
236_L244_E0.5420.27
41_V160_S0.5420.27
169_K237_K0.5420.27
185_E204_T0.5410.27
130_I169_K0.5390.27
204_T209_C0.5380.27
182_V203_C0.5380.27
194_K214_N0.5380.27
179_A217_I0.5360.27
32_S154_A0.5360.27
122_V145_L0.5360.27
51_S140_S0.5350.27
15_L208_E0.5340.27
102_A107_R0.5310.26
162_S166_Y0.5290.26
239_E243_L0.5280.26
105_E113_D0.5270.26
28_I246_G0.5270.26
179_A195_L0.5260.26
147_L244_E0.5260.26
176_C179_A0.5250.26
187_V207_E0.5240.26
101_E105_E0.5240.26
8_K110_Y0.5240.26
61_R155_K0.5230.26
256_L259_K0.5220.26
185_E188_F0.5220.26
185_E209_C0.5210.26
119_P123_P0.5210.26
9_D257_E0.5200.26
13_I245_A0.5190.26
133_L246_G0.5180.26
50_N168_P0.5180.26
97_Y142_E0.5170.25
152_E167_Y0.5170.25
115_K141_L0.5160.25
47_I88_N0.5140.25
19_G128_I0.5140.25
82_C88_N0.5130.25
24_F106_P0.5120.25
148_G215_G0.5110.25
7_H12_R0.5100.25
13_I239_E0.5100.25
45_Y142_E0.5100.25
179_A208_E0.5090.25
208_E212_Y0.5090.25
23_E214_N0.5090.25
242_L246_G0.5090.25
23_E152_E0.5080.25
185_E210_L0.5080.25
171_E220_S0.5070.25
205_L208_E0.5070.25
173_L195_L0.5070.25
76_Y191_K0.5060.25
70_E190_L0.5040.25
42_D144_R0.5030.25
47_I132_L0.5030.25
205_L210_L0.5010.24
51_S95_K0.5000.24
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  
2pa8D 1 0.9962 100 0.246 Contact Map
4c2mC 1 0.9849 100 0.256 Contact Map
4qjvA 1 0.9547 100 0.316 Contact Map
3h0gC 1 0.9245 100 0.358 Contact Map
1twfC 1 0.9472 100 0.359 Contact Map
4noiA 2 0.8113 100 0.518 Contact Map
2a6hA 2 0.7962 100 0.524 Contact Map
1bdfA 4 0.8075 100 0.533 Contact Map
4yfkA 2 0.8453 100 0.537 Contact Map
1xerA 2 0.3283 93.5 0.939 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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