GREMLIN Database
SIGI - RNA polymerase sigma factor SigI
UniProt: O31654 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 251 (227)
Sequences: 300 (256)
Seq/√Len: 17.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
198_L228_I5.5051.00
48_V66_G4.4451.00
33_Q75_E3.7671.00
24_S29_N3.5901.00
191_H212_L3.4010.99
33_Q71_N3.2410.99
56_I63_F3.1020.99
162_L228_I3.0840.99
188_L231_C2.9650.98
150_I164_F2.9030.98
21_A25_I2.8870.98
25_I32_L2.8200.98
97_V101_I2.8030.98
206_V220_I2.8010.98
188_L209_L2.7520.98
72_E96_K2.7130.97
82_G238_Y2.6380.97
88_F95_R2.6140.97
160_Y197_I2.5630.96
175_T179_Q2.5430.96
99_D102_R2.4330.95
25_I29_N2.2240.92
230_M245_L2.2100.91
44_I70_F2.2020.91
77_Y233_I2.1910.91
219_T223_N2.1510.90
164_F233_I1.9530.85
54_R60_D1.9210.84
157_L162_L1.8980.84
146_R244_Y1.7990.80
52_C137_Y1.6700.75
25_I36_L1.6490.74
63_F223_N1.6160.72
21_A32_L1.6130.72
33_Q74_I1.5790.70
146_R240_Y1.5770.70
160_Y199_Y1.5760.70
58_E63_F1.5440.69
177_A195_A1.5440.69
221_E224_R1.4820.65
186_M191_H1.4650.64
112_N116_Q1.4170.62
71_N75_E1.3910.60
99_D224_R1.3810.60
43_F98_I1.3800.60
46_K225_K1.3540.58
66_G97_V1.3390.57
60_D171_S1.3190.56
162_L198_L1.3190.56
25_I37_I1.3130.56
217_R221_E1.3010.55
22_V86_L1.3010.55
193_E208_Q1.2940.55
27_K153_F1.2860.54
117_E230_M1.2840.54
32_L37_I1.2790.54
181_A223_N1.2730.53
36_L177_A1.2690.53
181_A227_I1.2640.53
68_I92_I1.2240.50
40_Y86_L1.2130.50
55_Y77_Y1.2100.50
204_L217_R1.1990.49
156_Q159_D1.1910.48
159_D202_K1.1880.48
140_Q143_Q1.1860.48
210_E217_R1.1740.47
65_I206_V1.1720.47
187_T209_L1.1710.47
181_A216_S1.1450.46
156_Q238_Y1.1340.45
37_I44_I1.1300.45
166_E170_N1.1290.45
101_I223_N1.1250.45
184_V215_V1.1190.44
94_K163_S1.1190.44
240_Y244_Y1.1110.44
101_I222_R1.1000.43
96_K161_G1.0910.43
65_I133_S1.0900.42
77_Y239_I1.0850.42
146_R178_R1.0770.42
56_I223_N1.0690.41
77_Y136_E1.0560.41
53_K92_I1.0500.40
42_P46_K1.0490.40
188_L194_L1.0480.40
76_K95_R1.0430.40
95_R223_N1.0400.40
191_H194_L1.0370.39
149_E240_Y1.0340.39
91_L95_R1.0340.39
35_E39_Q1.0250.39
85_L92_I1.0250.39
194_L209_L1.0200.38
164_F222_R1.0190.38
160_Y209_L1.0160.38
91_L232_I1.0090.38
133_S178_R1.0060.38
51_V97_V1.0050.38
49_S55_Y1.0030.37
113_I153_F0.9980.37
149_E222_R0.9940.37
177_A181_A0.9890.37
36_L128_I0.9810.36
166_E234_I0.9790.36
133_S146_R0.9740.36
188_L195_A0.9720.36
204_L216_S0.9710.36
176_D219_T0.9670.35
175_T220_I0.9650.35
133_S226_Y0.9640.35
81_K192_E0.9630.35
99_D221_E0.9540.35
92_I167_L0.9530.35
21_A39_Q0.9510.35
48_V68_I0.9480.34
61_D68_I0.9470.34
20_K120_D0.9440.34
22_V226_Y0.9420.34
77_Y116_Q0.9310.34
71_N176_D0.9290.33
66_G239_I0.9230.33
189_V233_I0.9190.33
106_R143_Q0.9170.33
59_K233_I0.9160.33
144_E184_V0.9150.33
220_I230_M0.9120.33
58_E168_L0.9090.32
228_I231_C0.9070.32
77_Y90_E0.9060.32
34_N236_G0.9040.32
77_Y208_Q0.9030.32
37_I90_E0.9010.32
62_E65_I0.8960.32
223_N226_Y0.8890.31
199_Y232_I0.8760.31
140_Q160_Y0.8750.31
28_G71_N0.8700.30
153_F238_Y0.8690.30
110_N175_T0.8680.30
37_I48_V0.8670.30
198_L231_C0.8660.30
27_K175_T0.8640.30
174_H178_R0.8620.30
40_Y219_T0.8590.30
147_R243_D0.8510.29
40_Y46_K0.8510.29
104_E107_S0.8500.29
99_D244_Y0.8490.29
177_A219_T0.8430.29
58_E133_S0.8430.29
96_K228_I0.8410.29
42_P88_F0.8390.29
113_I238_Y0.8350.29
157_L187_T0.8290.28
68_I240_Y0.8280.28
177_A180_N0.8260.28
27_K103_K0.8190.28
178_R216_S0.8100.27
20_K119_D0.8090.27
177_A231_C0.8090.27
206_V218_K0.8030.27
28_G185_A0.8010.27
45_A63_F0.7990.27
97_V213_V0.7990.27
20_K24_S0.7960.27
226_Y235_T0.7960.27
237_D243_D0.7930.27
176_D182_I0.7920.27
111_I166_E0.7910.27
26_Q63_F0.7870.26
77_Y134_I0.7860.26
101_I166_E0.7810.26
98_I102_R0.7780.26
158_K161_G0.7780.26
181_A213_V0.7710.26
104_E113_I0.7700.26
92_I96_K0.7700.26
143_Q196_A0.7700.26
42_P86_L0.7670.25
72_E92_I0.7650.25
216_S226_Y0.7640.25
55_Y82_G0.7620.25
23_E77_Y0.7610.25
65_I220_I0.7610.25
238_Y242_K0.7600.25
184_V220_I0.7600.25
105_A171_S0.7550.25
184_V202_K0.7540.25
26_Q239_I0.7530.25
52_C239_I0.7530.25
41_K223_N0.7500.25
44_I238_Y0.7470.25
169_E215_V0.7450.24
60_D89_A0.7430.24
43_F70_F0.7420.24
45_A137_Y0.7390.24
39_Q75_E0.7370.24
57_D108_A0.7350.24
97_V125_Q0.7330.24
76_K88_F0.7270.24
134_I194_L0.7230.23
17_T35_E0.7200.23
41_K217_R0.7190.23
90_E94_K0.7180.23
37_I70_F0.7170.23
80_E209_L0.7140.23
36_L181_A0.7120.23
56_I216_S0.7100.23
146_R217_R0.7070.23
234_I237_D0.7060.23
83_N241_L0.7060.23
25_I223_N0.6990.22
195_A231_C0.6990.22
61_D198_L0.6980.22
26_Q78_S0.6960.22
215_V222_R0.6950.22
64_S71_N0.6920.22
17_T37_I0.6890.22
45_A223_N0.6880.22
113_I232_I0.6880.22
169_E194_L0.6850.22
105_A154_Q0.6820.22
153_F162_L0.6820.22
107_S202_K0.6800.22
171_S234_I0.6790.22
168_L171_S0.6780.22
196_A200_T0.6780.22
191_H228_I0.6770.22
87_A100_Y0.6740.21
194_L225_K0.6740.21
214_S220_I0.6700.21
63_F174_H0.6660.21
205_P225_K0.6650.21
63_F100_Y0.6600.21
64_S67_L0.6540.21
61_D153_F0.6530.21
171_S217_R0.6470.20
29_N48_V0.6470.20
176_D223_N0.6450.20
35_E135_D0.6410.20
48_V97_V0.6390.20
19_E26_Q0.6350.20
136_E193_E0.6330.20
79_P242_K0.6320.20
195_A235_T0.6320.20
20_K191_H0.6290.20
34_N83_N0.6290.20
46_K219_T0.6250.20
129_E211_Q0.6210.19
47_T71_N0.6200.19
52_C181_A0.6200.19
33_Q162_L0.6190.19
23_E44_I0.6160.19
90_E95_R0.6160.19
161_G168_L0.6160.19
98_I244_Y0.6150.19
200_T245_L0.6130.19
36_L143_Q0.6110.19
163_S187_T0.6110.19
100_Y188_L0.6040.19
37_I244_Y0.6030.19
33_Q243_D0.6020.19
50_S94_K0.6010.19
120_D134_I0.5980.19
136_E208_Q0.5980.19
180_N215_V0.5980.19
94_K98_I0.5970.19
118_G121_Q0.5970.19
61_D224_R0.5970.19
67_L241_L0.5940.18
171_S241_L0.5940.18
44_I82_G0.5940.18
125_Q230_M0.5940.18
142_E147_R0.5920.18
153_F157_L0.5880.18
154_Q238_Y0.5880.18
155_K211_Q0.5870.18
65_I225_K0.5860.18
22_V127_L0.5850.18
107_S110_N0.5820.18
176_D181_A0.5810.18
17_T235_T0.5810.18
137_Y225_K0.5790.18
42_P61_D0.5790.18
115_L128_I0.5760.18
33_Q167_L0.5760.18
87_A238_Y0.5740.18
210_E226_Y0.5730.18
156_Q164_F0.5720.18
72_E215_V0.5680.17
165_K193_E0.5680.17
78_S84_S0.5670.17
101_I243_D0.5630.17
26_Q60_D0.5610.17
26_Q29_N0.5610.17
95_R219_T0.5600.17
67_L129_E0.5590.17
91_L166_E0.5570.17
146_R164_F0.5540.17
66_G163_S0.5540.17
177_A216_S0.5530.17
102_R229_A0.5510.17
186_M190_E0.5500.17
65_I175_T0.5490.17
63_F219_T0.5490.17
19_E66_G0.5460.17
40_Y101_I0.5460.17
41_K226_Y0.5450.17
155_K245_L0.5450.17
183_K192_E0.5430.17
52_C62_E0.5410.17
28_G219_T0.5410.17
137_Y233_I0.5410.17
28_G129_E0.5400.17
80_E215_V0.5390.17
105_A135_D0.5390.17
31_D131_E0.5380.16
154_Q226_Y0.5370.16
160_Y196_A0.5330.16
40_Y84_S0.5320.16
58_E223_N0.5290.16
48_V95_R0.5260.16
75_E232_I0.5240.16
121_Q175_T0.5240.16
106_R152_Y0.5240.16
94_K244_Y0.5160.16
184_V208_Q0.5150.16
163_S168_L0.5150.16
184_V228_I0.5130.16
112_N115_L0.5120.16
22_V28_G0.5120.16
97_V177_A0.5100.16
121_Q136_E0.5080.16
154_Q224_R0.5070.15
183_K191_H0.5060.15
125_Q179_Q0.5050.15
98_I221_E0.5000.15
116_Q119_D0.5000.15
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  
1l0oC 1 0.1514 99.4 0.838 Contact Map
4yfkF 1 0.9522 99.3 0.849 Contact Map
4nqwA 1 0.5896 99.3 0.85 Contact Map
1rp3A 1 0.8446 99.2 0.855 Contact Map
1l9zH 1 0.9283 99.2 0.856 Contact Map
2a6hF 1 0.9163 99.2 0.857 Contact Map
1or7A 2 0.7251 99.1 0.862 Contact Map
2q1zA 1 0.6972 99 0.867 Contact Map
1sigA 1 0.4104 98.9 0.869 Contact Map
4x8kA 1 0.4143 98.9 0.87 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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