GREMLIN Database
SIGA - RNA polymerase sigma factor SigA
UniProt: P06224 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 371 (325)
Sequences: 3102 (1348)
Seq/√Len: 74.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
315_E319_R4.9691.00
229_L233_L4.8941.00
235_R241_E4.7921.00
232_D245_D4.5401.00
240_E250_P4.1651.00
222_L246_M3.6911.00
319_R325_D3.4311.00
242_I253_V3.1641.00
339_F346_I3.1421.00
136_R140_E2.9801.00
122_A126_K2.9641.00
276_S281_F2.9261.00
341_V346_I2.8651.00
302_Q369_F2.7641.00
105_Y120_E2.7231.00
145_L187_S2.7021.00
359_H362_R2.6681.00
116_S119_E2.6611.00
314_E356_K2.4131.00
128_E181_R2.3961.00
225_V246_M2.3811.00
128_E180_Y2.3471.00
126_K131_D2.2361.00
333_E342_T2.2031.00
345_R348_Q2.1701.00
229_L242_I2.1511.00
316_N338_V2.1011.00
222_L242_I2.0361.00
344_E347_R2.0081.00
239_P257_L2.0041.00
229_L237_P1.9921.00
114_L120_E1.9831.00
321_R350_E1.9611.00
229_L235_R1.9531.00
105_Y110_G1.9431.00
112_V141_A1.8371.00
135_K176_E1.8321.00
105_Y168_N1.8201.00
100_D120_E1.8131.00
105_Y109_I1.7801.00
308_D315_E1.7681.00
309_T362_R1.7651.00
233_L241_E1.7551.00
137_R141_A1.7511.00
67_N70_T1.7121.00
100_D105_Y1.6851.00
174_A190_A1.6561.00
115_L120_E1.6331.00
119_E137_R1.6271.00
320_L330_R1.6030.99
110_G120_E1.5990.99
332_L344_E1.5970.99
243_A253_V1.5770.99
105_Y114_L1.5540.99
177_K217_E1.5530.99
149_I191_T1.5470.99
179_D182_K1.5280.99
306_V366_L1.5140.99
101_P120_E1.5110.99
322_F354_L1.5010.99
335_V339_F1.4880.99
120_E124_A1.4860.99
47_D61_V1.4640.99
300_K304_E1.4640.99
326_D330_R1.4620.99
105_Y124_A1.4530.99
56_L60_G1.4480.99
344_E348_Q1.4380.99
345_R349_I1.4340.99
138_L211_I1.4130.99
55_F59_Q1.4090.99
64_I68_E1.3990.99
229_L241_E1.3880.98
225_V245_D1.3840.98
117_A121_I1.3700.98
104_M108_E1.3650.98
331_T342_T1.3580.98
145_L188_T1.3570.98
187_S200_R1.3570.98
109_I147_V1.3330.98
316_N339_F1.3320.98
228_Q245_D1.3140.98
121_I125_Q1.3140.98
332_L348_Q1.3110.98
147_V272_E1.3060.98
139_A175_V1.3010.98
332_L347_R1.3010.98
50_D53_Y1.2930.98
226_Q257_L1.2920.98
330_R338_V1.2880.98
243_A250_P1.2710.97
75_I79_A1.2600.97
65_S69_E1.2520.97
46_S66_E1.2510.97
126_K137_R1.2460.97
336_G342_T1.2430.97
304_E325_D1.2330.97
320_L338_V1.2280.97
173_K177_K1.2250.97
106_L109_I1.2210.97
332_L336_G1.2160.97
68_E80_K1.2150.96
237_P241_E1.2140.96
60_G64_I1.2110.96
83_E86_D1.2080.96
169_M172_M1.2010.96
312_D315_E1.1940.96
49_M52_Y1.1900.96
60_G68_E1.1870.96
73_P77_Q1.1770.96
101_P105_Y1.1650.96
48_Q55_F1.1580.95
53_Y63_L1.1530.95
196_Q214_H1.1350.95
211_I259_I1.1260.95
125_Q180_Y1.1250.95
200_R217_E1.1130.94
51_E65_S1.1110.94
122_A129_E1.1070.94
186_F190_A1.1070.94
188_T191_T1.1030.94
298_L302_Q1.0950.94
225_V228_Q1.0940.94
53_Y56_L1.0940.94
146_V167_G1.0930.94
63_L66_E1.0890.94
216_V220_N1.0830.93
100_D110_G1.0830.93
317_V353_A1.0800.93
332_L350_E1.0740.93
156_R220_N1.0720.93
114_L144_R1.0690.93
45_E59_Q1.0690.93
200_R214_H1.0640.93
45_E49_M1.0610.93
64_I71_E1.0610.93
106_L110_G1.0540.92
100_D114_L1.0520.92
211_I215_M1.0500.92
331_T343_R1.0500.92
238_T241_E1.0410.92
223_I253_V1.0350.92
45_E54_E1.0330.92
139_A172_M1.0270.91
45_E48_Q1.0170.91
123_Y127_I1.0120.91
218_T252_K1.0100.91
65_S71_E1.0080.91
99_N102_V1.0050.91
48_Q59_Q1.0040.90
321_R332_L1.0010.90
318_L353_A1.0010.90
298_L301_E1.0010.90
67_N72_D1.0000.90
297_E301_E0.9960.90
295_A298_L0.9910.90
51_E55_F0.9910.90
71_E75_I0.9900.90
343_R348_Q0.9900.90
123_Y134_S0.9900.90
51_E57_G0.9890.90
113_N116_S0.9730.89
101_P115_L0.9730.89
336_G348_Q0.9700.89
48_Q66_E0.9640.89
219_I341_V0.9630.89
100_D104_M0.9630.89
220_N227_R0.9610.88
233_L237_P0.9610.88
239_P254_R0.9600.88
57_G60_G0.9580.88
68_E71_E0.9540.88
188_T200_R0.9440.88
200_R213_V0.9440.88
49_M61_V0.9440.88
114_L124_A0.9360.87
355_R360_P0.9340.87
100_D115_L0.9220.86
65_S68_E0.9220.86
56_L61_V0.9190.86
55_F58_E0.9150.86
317_V339_F0.9100.86
110_G124_A0.9090.86
212_P323_G0.9090.86
148_S151_K0.9080.85
341_V352_K0.9080.85
48_Q58_E0.9050.85
51_E58_E0.8980.85
54_E57_G0.8980.85
346_I361_S0.8950.85
158_M201_A0.8920.84
76_Q79_A0.8910.84
270_I281_F0.8890.84
46_S53_Y0.8860.84
45_E64_I0.8830.84
311_T356_K0.8820.84
342_T345_R0.8820.84
174_A186_F0.8800.84
185_K204_D0.8800.84
156_R207_R0.8790.84
267_E277_H0.8760.83
243_A248_L0.8750.83
154_V159_L0.8740.83
51_E56_L0.8720.83
253_V256_I0.8720.83
64_I69_E0.8700.83
215_M219_I0.8680.83
125_Q181_R0.8670.83
57_G68_E0.8660.83
336_G344_E0.8630.82
210_R214_H0.8590.82
55_F61_V0.8510.82
49_M53_Y0.8480.81
316_N320_L0.8450.81
182_K195_R0.8430.81
191_T342_T0.8420.81
46_S55_F0.8390.81
52_Y66_E0.8380.81
211_I219_I0.8330.80
119_E123_Y0.8320.80
152_R202_I0.8310.80
113_N120_E0.8310.80
49_M54_E0.8300.80
105_Y108_E0.8300.80
64_I67_N0.8270.80
219_I256_I0.8270.80
66_E71_E0.8270.80
148_S165_Q0.8240.79
336_G345_R0.8210.79
45_E71_E0.8200.79
328_R334_E0.8180.79
332_L345_R0.8150.79
104_M120_E0.8140.79
126_K134_S0.8100.78
70_T75_I0.8080.78
67_N73_P0.8070.78
84_E88_N0.8070.78
46_S51_E0.8040.78
45_E51_E0.8040.78
65_S79_A0.8030.78
88_N93_P0.8030.78
145_L200_R0.8030.78
67_N71_E0.8010.77
47_D60_G0.8000.77
60_G69_E0.7960.77
47_D71_E0.7960.77
302_Q305_D0.7960.77
177_K205_Q0.7910.77
61_V71_E0.7900.76
86_D90_L0.7890.76
65_S70_T0.7890.76
64_I77_Q0.7890.76
53_Y59_Q0.7880.76
268_T278_L0.7870.76
51_E72_D0.7850.76
349_I352_K0.7850.76
70_T73_P0.7810.76
270_I277_H0.7780.75
85_F89_D0.7780.75
147_V161_L0.7770.75
53_Y57_G0.7760.75
57_G64_I0.7760.75
72_D77_Q0.7750.75
82_E86_D0.7720.75
102_V110_G0.7700.75
75_I80_K0.7680.74
77_Q80_K0.7670.74
53_Y61_V0.7660.74
62_E71_E0.7640.74
59_Q63_L0.7640.74
269_P279_G0.7630.74
88_N91_S0.7620.74
51_E60_G0.7620.74
115_L123_Y0.7610.74
56_L64_I0.7550.73
218_T256_I0.7540.73
336_G347_R0.7520.73
109_I112_V0.7510.73
73_P80_K0.7500.73
135_K165_Q0.7490.73
60_G120_E0.7440.72
246_M253_V0.7430.72
289_S293_H0.7430.72
94_P97_K0.7430.72
46_S60_G0.7430.72
54_E58_E0.7420.72
45_E55_F0.7390.72
66_E70_T0.7380.71
255_E303_L0.7360.71
105_Y115_L0.7360.71
228_Q232_D0.7350.71
342_T352_K0.7350.71
69_E73_P0.7340.71
106_L120_E0.7330.71
61_V68_E0.7300.71
51_E54_E0.7290.71
75_I78_L0.7270.70
82_E85_F0.7260.70
199_T217_E0.7250.70
73_P79_A0.7230.70
215_M322_F0.7210.70
313_R345_R0.7200.70
54_E72_D0.7180.69
52_Y68_E0.7180.69
68_E79_A0.7180.69
193_W347_R0.7180.69
110_G114_L0.7170.69
57_G71_E0.7140.69
252_K255_E0.7120.69
61_V70_T0.7120.69
363_S367_K0.7100.69
70_T77_Q0.7000.67
304_E319_R0.6970.67
138_L175_V0.6970.67
105_Y112_V0.6930.67
351_A360_P0.6920.67
354_L358_R0.6860.66
173_K216_V0.6850.66
81_A89_D0.6850.66
143_L166_E0.6840.66
127_I131_D0.6820.65
143_L168_N0.6810.65
176_E329_T0.6810.65
51_E59_Q0.6790.65
151_K160_F0.6790.65
57_G70_T0.6770.65
49_M55_F0.6760.65
48_Q60_G0.6740.65
214_H217_E0.6730.64
185_K217_E0.6730.64
98_I102_V0.6730.64
46_S64_I0.6730.64
145_L191_T0.6720.64
332_L342_T0.6720.64
298_L327_G0.6700.64
61_V67_N0.6670.64
56_L67_N0.6630.63
47_D52_Y0.6630.63
57_G61_V0.6610.63
53_Y72_D0.6590.63
45_E57_G0.6580.63
332_L343_R0.6560.62
64_I80_K0.6540.62
64_I70_T0.6540.62
52_Y60_G0.6530.62
130_G133_E0.6490.62
105_Y117_A0.6490.62
192_W196_Q0.6490.62
105_Y113_N0.6480.61
222_L257_L0.6460.61
51_E69_E0.6450.61
56_L66_E0.6440.61
121_I181_R0.6430.61
293_H297_E0.6430.61
57_G63_L0.6420.61
187_S214_H0.6420.61
187_S191_T0.6410.61
89_D92_V0.6380.60
46_S69_E0.6380.60
59_Q72_D0.6380.60
191_T204_D0.6360.60
59_Q68_E0.6360.60
68_E75_I0.6350.60
253_V273_E0.6350.60
61_V64_I0.6350.60
45_E72_D0.6340.60
114_L130_G0.6340.60
48_Q53_Y0.6330.60
166_E205_Q0.6330.60
172_M176_E0.6310.59
215_M256_I0.6310.59
69_E75_I0.6280.59
266_L279_G0.6270.59
47_D73_P0.6250.59
84_E89_D0.6240.59
110_G121_I0.6220.58
53_Y58_E0.6200.58
66_E73_P0.6190.58
339_F352_K0.6170.58
76_Q80_K0.6170.58
53_Y66_E0.6160.58
76_Q86_D0.6140.57
54_E68_E0.6130.57
147_V168_N0.6110.57
117_A127_I0.6070.57
184_Y258_K0.6060.56
47_D58_E0.6050.56
199_T214_H0.6040.56
48_Q54_E0.6040.56
62_E65_S0.6040.56
50_D65_S0.6030.56
175_V272_E0.6000.56
46_S59_Q0.6000.56
55_F60_G0.6000.56
46_S50_D0.5990.56
235_R238_T0.5980.55
53_Y62_E0.5980.55
101_P114_L0.5970.55
81_A84_E0.5970.55
175_V291_S0.5960.55
154_V264_V0.5960.55
48_Q61_V0.5940.55
194_I198_I0.5940.55
263_P279_G0.5920.55
337_K340_G0.5920.55
303_L306_V0.5900.54
106_L113_N0.5880.54
153_Y157_G0.5860.54
193_W344_E0.5850.54
246_M316_N0.5850.54
59_Q65_S0.5840.54
51_E67_N0.5830.54
115_L124_A0.5820.53
67_N78_L0.5820.53
64_I73_P0.5760.53
45_E61_V0.5750.53
55_F66_E0.5740.52
199_T204_D0.5720.52
55_F62_E0.5720.52
130_G134_S0.5720.52
48_Q63_L0.5710.52
342_T348_Q0.5700.52
302_Q365_R0.5680.52
264_V268_T0.5670.52
48_Q51_E0.5670.52
291_S358_R0.5640.51
60_G73_P0.5630.51
72_D79_A0.5600.51
54_E65_S0.5550.50
47_D57_G0.5540.50
58_E71_E0.5530.50
59_Q70_T0.5530.50
52_Y77_Q0.5520.50
313_R332_L0.5520.50
222_L225_V0.5520.50
61_V72_D0.5500.49
45_E65_S0.5480.49
59_Q71_E0.5480.49
60_G65_S0.5470.49
154_V216_V0.5470.49
178_F227_R0.5460.49
246_M282_I0.5460.49
220_N223_I0.5450.49
127_I285_Q0.5450.49
314_E352_K0.5440.49
101_P158_M0.5440.49
49_M63_L0.5440.49
205_Q220_N0.5440.49
61_V65_S0.5410.48
318_L351_A0.5410.48
51_E61_V0.5400.48
112_V120_E0.5400.48
54_E61_V0.5400.48
71_E78_L0.5400.48
83_E93_P0.5400.48
153_Y290_P0.5390.48
70_T79_A0.5380.48
200_R331_T0.5380.48
45_E53_Y0.5370.48
54_E70_T0.5350.48
82_E87_L0.5340.47
57_G72_D0.5340.47
71_E77_Q0.5340.47
156_R369_F0.5320.47
198_I206_A0.5300.47
46_S57_G0.5280.47
239_P253_V0.5260.46
48_Q72_D0.5260.46
267_E278_L0.5260.46
48_Q118_K0.5240.46
148_S203_A0.5230.46
187_S213_V0.5220.46
66_E69_E0.5220.46
52_Y56_L0.5220.46
261_Q324_L0.5170.45
72_D80_K0.5160.45
214_H343_R0.5150.45
69_E72_D0.5140.45
173_K197_A0.5140.45
57_G340_G0.5090.44
81_A85_F0.5090.44
60_G70_T0.5080.44
191_T214_H0.5070.44
267_E283_E0.5050.44
188_T215_M0.5050.44
305_D325_D0.5000.43
185_K261_Q0.5000.43
333_E337_K0.5000.43
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  
1l9zH 1 0.7116 100 0.355 Contact Map
2a6hF 1 0.7332 100 0.361 Contact Map
4yfkF 1 0.7385 100 0.367 Contact Map
3ugoA 1 0.2965 100 0.633 Contact Map
1l0oC 1 0.1536 100 0.656 Contact Map
1rp3A 1 0.6173 100 0.682 Contact Map
1sigA 1 0.5256 99.9 0.764 Contact Map
4x8kA 1 0.2453 99.9 0.787 Contact Map
4nqwA 1 0.3989 99.9 0.788 Contact Map
1or7A 2 0.496 99.8 0.814 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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