GREMLIN Database
SIGO - RNA polymerase sigma factor SigO
UniProt: O34843 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 176 (167)
Sequences: 108 (106)
Seq/√Len: 8.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
133_Y157_H5.3931.00
26_P30_D3.1640.91
63_D67_R2.8970.86
148_E152_N2.8930.86
150_R155_N2.8420.85
122_T153_I2.6260.80
43_K47_I2.5550.78
35_D39_K2.5070.77
139_M150_R2.4780.76
109_V118_I2.4280.74
152_N155_N2.3340.71
58_F61_D2.0640.61
125_Q133_Y2.0390.60
61_D64_K2.0270.60
15_H23_M1.9510.57
152_N156_I1.9500.57
125_Q157_H1.9300.56
15_H18_L1.8930.54
3_H161_L1.8590.53
54_M139_M1.8430.52
59_S161_L1.7680.49
62_F67_R1.7650.49
56_R159_K1.7570.49
55_I111_D1.7070.47
160_G163_N1.6960.46
148_E153_I1.6950.46
51_M62_F1.6920.46
39_K45_I1.6850.46
50_Y59_S1.6810.45
54_M59_S1.6630.45
60_I111_D1.6240.43
139_M155_N1.5990.42
149_S152_N1.5860.42
139_M152_N1.5790.41
132_V139_M1.5720.41
111_D136_G1.5700.41
45_I164_I1.4840.38
141_E150_R1.4620.37
60_I133_Y1.4480.36
84_D116_Q1.4330.36
61_D155_N1.4200.35
46_R142_I1.4090.35
42_Y109_V1.4050.35
49_K53_S1.3990.34
43_K139_M1.3950.34
164_I168_L1.3780.34
56_R63_D1.3680.33
105_L134_L1.3530.33
5_I44_E1.3510.33
52_N152_N1.3480.32
47_I155_N1.3400.32
10_L122_T1.3370.32
19_F127_S1.3110.31
59_S63_D1.2910.30
5_I75_L1.2900.30
54_M58_F1.2710.30
50_Y146_L1.2660.30
15_H73_Y1.2610.29
3_H45_I1.2380.29
132_V157_H1.2360.28
132_V142_I1.2170.28
62_F149_S1.2070.28
148_E156_I1.1920.27
30_D125_Q1.1850.27
140_Q150_R1.1680.26
26_P77_V1.1660.26
56_R85_R1.1380.25
4_P35_D1.1300.25
140_Q154_S1.1230.25
54_M152_N1.1180.25
16_Y19_F1.1150.25
75_L147_G1.1010.24
129_L154_S1.0890.24
80_P114_L1.0790.23
48_V81_E1.0610.23
129_L164_I1.0520.23
76_T107_Q1.0520.23
7_K78_D1.0510.23
18_L35_D1.0460.23
126_K155_N1.0420.22
8_H41_F1.0390.22
110_Q130_T1.0280.22
10_L19_F1.0250.22
47_I133_Y1.0250.22
55_I140_Q1.0240.22
117_A133_Y0.9880.21
33_S165_R0.9810.21
25_S105_L0.9810.21
50_Y62_F0.9760.21
72_R125_Q0.9640.20
7_K72_R0.9630.20
14_Q161_L0.9570.20
35_D154_S0.9560.20
15_H161_L0.9450.20
102_Q153_I0.9330.19
128_V156_I0.9320.19
43_K125_Q0.9260.19
22_V96_E0.9200.19
34_L158_K0.9190.19
15_H51_M0.9110.19
86_L135_H0.9100.19
47_I117_A0.8990.19
108_H157_H0.8980.19
117_A125_Q0.8810.18
142_I150_R0.8810.18
53_S130_T0.8770.18
47_I72_R0.8750.18
54_M61_D0.8620.18
34_L131_K0.8620.18
121_L125_Q0.8620.18
124_K134_L0.8560.17
99_L117_A0.8550.17
4_P147_G0.8550.17
22_V122_T0.8520.17
140_Q156_I0.8510.17
56_R65_R0.8440.17
106_S149_S0.8350.17
89_E154_S0.8330.17
80_P131_K0.8170.17
27_N30_D0.8160.17
75_L164_I0.8090.16
25_S96_E0.8050.16
59_S117_A0.7990.16
19_F139_M0.7970.16
33_S118_I0.7910.16
19_F43_K0.7820.16
119_Q147_G0.7790.16
25_S114_L0.7720.16
118_I137_A0.7690.16
62_F142_I0.7680.15
3_H52_N0.7680.15
34_L155_N0.7620.15
14_Q55_I0.7570.15
20_K86_L0.7560.15
43_K155_N0.7540.15
148_E155_N0.7520.15
34_L41_F0.7460.15
46_R152_N0.7450.15
36_E111_D0.7420.15
131_K157_H0.7340.15
55_I125_Q0.7330.15
26_P122_T0.7290.15
10_L26_P0.7270.15
54_M129_L0.7240.15
35_D54_M0.7210.14
21_N128_V0.7180.14
3_H46_R0.7160.14
48_V153_I0.7160.14
44_E127_S0.7140.14
46_R159_K0.7110.14
53_S156_I0.7100.14
29_K168_L0.7010.14
29_K93_D0.7000.14
3_H8_H0.6990.14
5_I32_R0.6900.14
5_I9_F0.6900.14
68_K128_V0.6880.14
37_L97_E0.6870.14
153_I156_I0.6850.14
42_Y59_S0.6850.14
6_V147_G0.6840.14
122_T125_Q0.6780.14
33_S45_I0.6750.14
36_E97_E0.6750.14
64_K157_H0.6750.14
31_A35_D0.6680.13
8_H12_N0.6630.13
58_F152_N0.6610.13
20_K39_K0.6590.13
100_D167_Q0.6590.13
26_P64_K0.6530.13
25_S44_E0.6530.13
125_Q155_N0.6520.13
13_P41_F0.6500.13
47_I139_M0.6490.13
109_V112_Y0.6480.13
5_I23_M0.6470.13
21_N25_S0.6470.13
52_N81_E0.6430.13
100_D153_I0.6390.13
145_S155_N0.6350.13
65_R128_V0.6340.13
29_K160_G0.6340.13
49_K77_V0.6340.13
88_S136_G0.6340.13
79_H114_L0.6290.13
117_A158_K0.6270.13
39_K63_D0.6260.13
49_K132_V0.6200.13
49_K163_N0.6200.13
52_N89_E0.6190.13
7_K57_I0.6120.12
32_R144_D0.6090.12
59_S140_Q0.6080.12
8_H15_H0.6070.12
57_I109_V0.6020.12
88_S143_A0.6010.12
102_Q107_Q0.6000.12
42_Y73_Y0.5990.12
137_A141_E0.5980.12
117_A168_L0.5970.12
80_P84_D0.5940.12
77_V137_A0.5930.12
123_D144_D0.5920.12
107_Q137_A0.5890.12
6_V163_N0.5890.12
19_F30_D0.5890.12
19_F153_I0.5870.12
42_Y93_D0.5830.12
39_K104_D0.5790.12
117_A121_L0.5700.12
24_E115_Y0.5690.12
37_L85_R0.5680.12
59_S105_L0.5650.12
41_F136_G0.5650.12
118_I164_I0.5650.12
120_K128_V0.5620.12
130_T135_H0.5610.11
28_E123_D0.5600.11
105_L135_H0.5570.11
107_Q139_M0.5490.11
5_I107_Q0.5460.11
75_L80_P0.5420.11
51_M70_Q0.5420.11
3_H110_Q0.5420.11
114_L144_D0.5410.11
57_I131_K0.5380.11
26_P129_L0.5370.11
34_L165_R0.5320.11
78_D159_K0.5290.11
69_N75_L0.5240.11
13_P40_Q0.5240.11
84_D125_Q0.5240.11
63_D105_L0.5230.11
46_R156_I0.5220.11
27_N77_V0.5210.11
53_S149_S0.5190.11
47_I152_N0.5160.11
111_D164_I0.5150.11
145_S161_L0.5120.11
46_R140_Q0.5110.11
59_S150_R0.5100.11
132_V140_Q0.5100.11
24_E124_K0.5090.11
10_L136_G0.5080.11
61_D117_A0.5070.11
49_K59_S0.5040.11
62_F84_D0.5020.11
47_I59_S0.5020.11
143_A151_Q0.5000.11
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  
4yfkF 1 0.9318 99.3 0.766 Contact Map
1l0oC 1 0.0511 99.3 0.769 Contact Map
4cxfA 1 0.7386 99.3 0.771 Contact Map
1rp3A 1 0.9091 99.2 0.773 Contact Map
4nqwA 1 0.7273 99.2 0.774 Contact Map
2a6hF 1 0.9091 99.2 0.779 Contact Map
1l9zH 1 0.8864 99.2 0.779 Contact Map
3mzyA 1 0.6761 99.2 0.779 Contact Map
1or7A 2 0.8977 99.2 0.779 Contact Map
2q1zA 1 0.8352 99.2 0.782 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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