GREMLIN Database
RP54 - RNA polymerase sigma-54 factor
UniProt: P24219 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 436 (424)
Sequences: 2280 (1603)
Seq/√Len: 77.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
234_I302_I4.4021.00
381_H408_H3.9851.00
304_E328_V3.4781.00
382_L400_L3.3051.00
148_A165_R3.2641.00
99_T134_E3.1221.00
238_V314_L3.1001.00
193_S200_L2.9681.00
300_R332_L2.9651.00
100_E138_V2.9441.00
107_L142_L2.9241.00
236_I348_I2.8271.00
324_T327_E2.8221.00
152_A161_L2.7841.00
153_R157_E2.7271.00
122_E132_A2.6811.00
121_I139_L2.6511.00
172_Q198_I2.6471.00
104_F142_L2.6411.00
97_T100_E2.4411.00
112_D118_E2.4281.00
176_L206_I2.3601.00
214_H219_L2.3451.00
164_Q174_E2.3271.00
100_E137_A2.3241.00
104_F138_V2.3061.00
111_L151_G2.3031.00
243_I314_L2.3001.00
304_E331_C2.2871.00
214_H220_L2.2601.00
139_L153_R2.2411.00
193_S203_I2.2261.00
302_I348_I2.2041.00
40_L283_E2.1961.00
334_L339_V2.1891.00
48_E258_H2.1821.00
230_I347_T2.1761.00
142_L151_G2.0991.00
86_A221_F2.0981.00
173_A206_I2.0941.00
312_F355_F2.0851.00
91_S108_I2.0801.00
103_I138_V2.0771.00
175_M179_A2.0751.00
139_L143_Q2.0601.00
398_Q402_D2.0521.00
304_E307_T2.0491.00
91_S104_F2.0491.00
382_L404_L2.0441.00
87_L108_I2.0191.00
132_A136_E1.9901.00
143_Q153_R1.9711.00
103_I135_A1.9651.00
199_P202_T1.9451.00
148_A161_L1.9241.00
403_L406_E1.9221.00
355_F359_L1.9201.00
100_E134_E1.9161.00
308_R323_L1.9151.00
310_K314_L1.9081.00
180_H196_T1.8831.00
111_L142_L1.8721.00
160_L174_E1.8671.00
385_L403_L1.8591.00
116_Y158_C1.8561.00
385_L400_L1.8521.00
81_K89_Q1.8371.00
120_D123_E1.7991.00
209_D212_A1.7961.00
161_L164_Q1.7891.00
386_I424_M1.7681.00
384_N388_Q1.7661.00
192_L203_I1.7621.00
183_A188_K1.7591.00
15_L22_A1.7351.00
125_A135_A1.7321.00
239_K242_H1.7141.00
198_I206_I1.7131.00
238_V243_I1.6861.00
325_L358_K1.6851.00
114_N118_E1.6751.00
270_C273_T1.6741.00
245_A306_I1.6711.00
107_L151_G1.6701.00
332_L339_V1.6551.00
100_E141_K1.6511.00
399_K403_L1.6401.00
183_A192_L1.6351.00
325_L343_I1.6291.00
383_E387_N1.6141.00
136_E153_R1.6101.00
163_L177_V1.6101.00
88_K105_N1.6051.00
121_I135_A1.5861.00
180_H183_A1.5770.99
124_A135_A1.5760.99
313_F350_T1.5720.99
91_S145_L1.5630.99
94_M145_L1.5590.99
172_Q206_I1.5530.99
103_I130_V1.5460.99
405_Y411_Q1.5440.99
181_F185_A1.5390.99
166_L209_D1.5340.99
356_E359_L1.5190.99
155_L158_C1.4930.99
237_T246_E1.4850.99
159_I213_L1.4850.99
139_L161_L1.4710.99
315_K319_A1.4680.99
104_F107_L1.4600.99
155_L216_R1.4570.99
236_I306_I1.4570.99
108_I145_L1.4340.99
308_R331_C1.4300.99
156_Q160_L1.4220.99
313_F351_P1.4140.99
41_S49_R1.3870.99
350_T353_G1.3800.99
87_L150_I1.3730.99
177_V181_F1.3660.99
163_L213_L1.3650.99
312_F360_F1.3600.98
235_F349_Q1.3570.98
116_Y155_L1.3560.98
143_Q157_E1.3560.98
183_A191_T1.3530.98
158_C218_G1.3410.98
116_Y216_R1.3360.98
13_P19_L1.3330.98
180_H195_E1.3200.98
156_Q181_F1.3180.98
160_L178_S1.3180.98
143_Q161_L1.3160.98
13_P16_T1.3120.98
323_L327_E1.3120.98
362_S374_S1.3080.98
318_S384_N1.3080.98
363_A375_N1.3060.98
355_F360_F1.3030.98
348_I351_P1.3030.98
20_R24_T1.2950.98
308_R327_E1.2830.98
395_L400_L1.2830.98
401_V405_Y1.2760.98
234_I348_I1.2740.98
36_Y40_L1.2670.98
156_Q178_S1.2660.98
160_L164_Q1.2650.98
121_I136_E1.2580.97
121_I132_A1.2420.97
300_R334_L1.2390.97
305_L323_L1.2370.97
152_A158_C1.2330.97
257_L284_W1.2270.97
163_L209_D1.2240.97
247_L299_T1.2240.97
306_I313_F1.2080.97
163_L173_A1.2060.97
83_L221_F1.1980.97
86_A146_E1.1930.97
204_Q208_D1.1900.96
131_S134_E1.1860.96
307_T331_C1.1820.96
198_I203_I1.1700.96
158_C216_R1.1530.96
399_K402_D1.1520.96
161_L165_R1.1470.96
303_N307_T1.1420.96
107_L135_A1.1360.95
114_N216_R1.1350.95
384_N408_H1.1170.95
181_F184_F1.1120.95
413_S416_T1.1040.95
311_D321_K1.0970.94
96_L141_K1.0960.94
41_S47_I1.0960.94
204_Q434_R1.0960.94
20_R336_E1.0880.94
90_Q147_P1.0880.94
238_V241_G1.0850.94
379_K423_Q1.0830.94
304_E308_R1.0720.94
312_F359_L1.0700.94
389_E394_P1.0680.94
138_V151_G1.0680.94
255_I288_S1.0630.93
188_K191_T1.0630.93
308_R328_V1.0590.93
183_A195_E1.0550.93
136_E140_A1.0530.93
90_Q145_L1.0510.93
348_I357_M1.0510.93
214_H218_G1.0490.93
326_R336_E1.0480.93
23_I286_W1.0410.93
386_I426_I1.0400.93
37_I41_S1.0360.93
84_Q109_H1.0300.92
15_L23_I1.0290.92
104_F145_L1.0280.92
302_I357_M1.0260.92
37_I287_L1.0240.92
107_L139_L1.0230.92
393_K399_K1.0210.92
25_L342_A1.0200.92
43_E280_K1.0180.92
390_D393_K1.0180.92
103_I134_E1.0170.92
92_L101_K1.0150.92
172_Q196_T1.0100.92
243_I313_F1.0100.92
173_A176_L0.9970.91
180_H192_L0.9910.91
82_T85_D0.9880.91
201_H204_Q0.9810.90
347_T356_E0.9790.90
106_Y124_A0.9780.90
239_K244_A0.9770.90
173_A209_D0.9760.90
158_C214_H0.9700.90
83_L218_G0.9620.90
356_E360_F0.9580.89
125_A132_A0.9550.89
404_L417_V0.9530.89
189_W203_I0.9470.89
301_I325_L0.9440.89
391_K434_R0.9430.89
169_R174_E0.9360.88
84_Q113_S0.9320.88
91_S96_L0.9310.88
29_H345_G0.9230.87
289_R336_E0.9190.87
91_S95_N0.9160.87
367_A373_A0.9160.87
208_D434_R0.9160.87
144_S161_L0.9160.87
139_L152_A0.9140.87
297_T342_A0.9130.87
367_A370_D0.9110.87
134_E137_A0.9110.87
174_E178_S0.9050.86
377_A410_I0.9040.86
36_Y287_L0.9000.86
104_F151_G0.8990.86
378_V404_L0.8960.86
300_R303_N0.8950.86
257_L262_R0.8940.86
257_L288_S0.8930.86
125_A130_V0.8890.85
311_D319_A0.8890.85
91_S101_K0.8880.85
402_D405_Y0.8870.85
305_L360_F0.8870.85
46_L281_Y0.8860.85
192_L195_E0.8850.85
87_L145_L0.8850.85
173_A210_I0.8780.85
200_L204_Q0.8710.84
249_T295_K0.8710.84
119_E123_E0.8710.84
234_I357_M0.8700.84
39_E43_E0.8690.84
286_W293_Q0.8640.84
390_D394_P0.8630.84
203_I207_S0.8550.83
107_L124_A0.8540.83
130_V135_A0.8540.83
45_P276_Y0.8510.83
395_L403_L0.8500.83
116_Y261_Y0.8500.83
380_T383_E0.8490.83
83_L86_A0.8460.82
330_D333_S0.8450.82
381_H384_N0.8430.82
298_I342_A0.8410.82
184_F189_W0.8410.82
41_S255_I0.8370.82
306_I348_I0.8370.82
141_K144_S0.8370.82
349_Q354_L0.8370.82
40_L287_L0.8360.82
144_S165_R0.8350.82
186_Q431_A0.8340.82
167_P170_N0.8250.81
304_E332_L0.8170.80
108_I142_L0.8140.80
104_F108_I0.8130.80
189_W207_S0.8110.80
16_T23_I0.8100.80
386_I389_E0.8070.79
281_Y285_R0.8070.79
235_F248_N0.8050.79
245_A302_I0.8050.79
117_L124_A0.8040.79
86_A89_Q0.8040.79
257_L281_Y0.8030.79
144_S164_Q0.8020.79
389_E432_R0.8020.79
47_I255_I0.8010.79
47_I284_W0.8010.79
325_L337_S0.7990.79
153_R161_L0.7970.79
160_L177_V0.7950.78
48_E256_D0.7930.78
243_I351_P0.7920.78
116_Y215_P0.7910.78
393_K430_A0.7890.78
41_S52_T0.7890.78
142_L161_L0.7880.78
138_V141_K0.7850.78
255_I291_L0.7820.77
23_I28_Y0.7810.77
365_A378_V0.7720.76
110_S119_E0.7710.76
156_Q182_D0.7700.76
383_E424_M0.7700.76
248_N253_P0.7680.76
296_Q300_R0.7680.76
367_A378_V0.7680.76
324_T363_A0.7660.76
37_I291_L0.7650.76
13_P23_I0.7650.76
299_T303_N0.7630.75
100_E103_I0.7620.75
18_E25_L0.7620.75
301_I356_E0.7590.75
84_Q88_K0.7560.75
385_L395_L0.7540.75
428_S431_A0.7520.74
90_Q146_E0.7520.74
71_E76_L0.7490.74
182_D186_Q0.7480.74
103_I128_L0.7460.74
192_L196_T0.7440.74
16_T20_R0.7440.74
72_A75_Q0.7420.73
387_N391_K0.7410.73
396_S399_K0.7370.73
106_Y127_R0.7340.73
234_I298_I0.7340.73
21_Q286_W0.7330.73
313_F352_Y0.7320.72
38_D42_L0.7320.72
28_Y36_Y0.7320.72
81_K86_A0.7310.72
271_Q274_V0.7310.72
166_L169_R0.7270.72
343_I361_F0.7260.72
176_L210_I0.7260.72
403_L408_H0.7260.72
187_K211_A0.7250.72
323_L363_A0.7220.71
234_I245_A0.7220.71
242_H310_K0.7220.71
18_E422_D0.7210.71
402_D406_E0.7190.71
96_L138_V0.7160.71
19_L23_I0.7130.70
170_N209_D0.7110.70
343_I358_K0.7080.70
359_L376_Y0.7080.70
202_T205_D0.7080.70
37_I349_Q0.7080.70
28_Y284_W0.7070.70
94_M141_K0.7060.70
292_R295_K0.7060.70
15_L431_A0.7040.69
22_A286_W0.7020.69
72_A77_S0.7020.69
50_K256_D0.7020.69
22_A25_L0.7010.69
172_Q175_M0.7010.69
138_V142_L0.7010.69
116_Y153_R0.6990.69
13_P20_R0.6980.69
317_R359_L0.6980.69
73_G77_S0.6960.69
19_L28_Y0.6960.69
284_W288_S0.6950.69
176_L203_I0.6950.69
323_L362_S0.6930.68
20_R349_Q0.6920.68
317_R352_Y0.6910.68
155_L400_L0.6910.68
7_Q281_Y0.6890.68
142_L145_L0.6850.67
222_A226_Q0.6830.67
136_E139_L0.6830.67
412_I417_V0.6820.67
200_L203_I0.6810.67
46_L261_Y0.6800.67
106_Y128_L0.6780.67
179_A205_D0.6760.66
418_A428_S0.6760.66
328_V342_A0.6700.66
37_I43_E0.6670.65
169_R209_D0.6670.65
84_Q111_L0.6670.65
326_R330_D0.6660.65
264_L378_V0.6650.65
184_F187_K0.6650.65
312_F317_R0.6630.65
315_K321_K0.6620.65
338_T341_R0.6610.65
222_A400_L0.6570.64
416_T419_K0.6570.64
32_E36_Y0.6560.64
362_S376_Y0.6550.64
173_A177_V0.6550.64
135_A139_L0.6530.64
128_L135_A0.6480.63
401_V412_I0.6470.63
418_A422_D0.6450.63
235_F251_S0.6440.63
139_L142_L0.6440.63
218_G360_F0.6400.62
120_D153_R0.6400.62
9_Q350_T0.6370.62
327_E330_D0.6360.62
158_C161_L0.6360.62
292_R296_Q0.6360.62
427_P431_A0.6360.62
298_I356_E0.6350.62
116_Y218_G0.6340.61
163_L170_N0.6330.61
345_G356_E0.6320.61
313_F359_L0.6320.61
68_N71_E0.6320.61
206_I210_I0.6320.61
9_Q36_Y0.6320.61
94_M339_V0.6310.61
311_D315_K0.6310.61
429_S434_R0.6310.61
34_A38_D0.6300.61
388_Q395_L0.6290.61
35_E39_E0.6290.61
189_W334_L0.6290.61
25_L344_K0.6290.61
328_V361_F0.6290.61
286_W290_A0.6280.61
364_K372_D0.6260.60
184_F210_I0.6260.60
301_I305_L0.6250.60
210_I328_V0.6240.60
293_Q298_I0.6240.60
368_S405_Y0.6230.60
281_Y284_W0.6220.60
189_W200_L0.6210.60
158_C215_P0.6210.60
69_A386_I0.6200.60
417_V422_D0.6200.60
365_A380_T0.6190.60
25_L247_L0.6180.59
308_R321_K0.6170.59
118_E154_S0.6160.59
117_L152_A0.6160.59
378_V412_I0.6150.59
208_D211_A0.6130.59
290_A298_I0.6120.59
426_I432_R0.6110.59
72_A76_L0.6110.59
176_L193_S0.6100.58
143_Q218_G0.6100.58
159_I177_V0.6090.58
343_I357_M0.6080.58
312_F356_E0.6070.58
156_Q177_V0.6070.58
174_E177_V0.6070.58
273_T276_Y0.6060.58
28_Y396_S0.6060.58
29_H298_I0.6060.58
260_Q264_L0.6060.58
175_M180_H0.6030.58
336_E418_A0.6030.58
400_L403_L0.6030.58
97_T138_V0.6020.57
199_P203_I0.6010.57
394_P432_R0.6000.57
153_R158_C0.6000.57
274_V278_S0.5990.57
250_R292_R0.5980.57
22_A210_I0.5980.57
230_I270_C0.5980.57
127_R424_M0.5980.57
289_R335_H0.5970.57
26_L335_H0.5970.57
245_A299_T0.5970.57
170_N177_V0.5960.57
418_A426_I0.5950.57
22_A335_H0.5940.56
91_S138_V0.5940.56
344_K358_K0.5930.56
328_V332_L0.5920.56
302_I306_I0.5910.56
19_L22_A0.5890.56
418_A430_A0.5880.56
272_D275_S0.5880.56
206_I256_D0.5880.56
14_Q17_Q0.5870.56
39_E369_G0.5870.56
243_I306_I0.5830.55
333_S386_I0.5830.55
20_R289_R0.5820.55
168_N209_D0.5800.55
19_L27_G0.5790.55
325_L340_S0.5770.54
154_S179_A0.5760.54
301_I342_A0.5750.54
301_I328_V0.5740.54
47_I288_S0.5730.54
106_Y110_S0.5720.54
98_N140_A0.5720.54
208_D212_A0.5710.54
354_L428_S0.5710.54
22_A396_S0.5700.53
75_Q78_N0.5690.53
137_A140_A0.5650.53
20_R37_I0.5650.53
120_D131_S0.5650.53
119_E127_R0.5640.53
123_E127_R0.5640.53
430_A433_K0.5640.53
140_A143_Q0.5630.53
286_W334_L0.5620.52
15_L429_S0.5610.52
27_G163_L0.5600.52
173_A181_F0.5600.52
289_R328_V0.5590.52
243_I352_Y0.5580.52
184_F423_Q0.5570.52
276_Y280_K0.5550.52
66_R69_A0.5540.51
139_L151_G0.5530.51
307_T310_K0.5530.51
316_G319_A0.5520.51
98_N101_K0.5520.51
267_S277_L0.5510.51
169_R173_A0.5490.51
346_K420_Y0.5480.51
375_N382_L0.5480.51
317_R380_T0.5470.50
18_E24_T0.5460.50
297_T332_L0.5460.50
265_L273_T0.5460.50
98_N102_K0.5460.50
263_T267_S0.5450.50
51_E58_S0.5440.50
101_K417_V0.5420.50
240_N266_S0.5410.50
318_S380_T0.5410.50
35_E38_D0.5410.50
184_F352_Y0.5390.49
20_R335_H0.5390.49
192_L198_I0.5390.49
233_D248_N0.5390.49
40_L47_I0.5380.49
37_I49_R0.5380.49
5_L374_S0.5370.49
178_S205_D0.5370.49
23_I324_T0.5360.49
89_Q93_D0.5350.49
46_L259_P0.5350.49
29_H258_H0.5350.49
237_T244_A0.5340.49
135_A138_V0.5340.49
46_L210_I0.5330.49
140_A164_Q0.5330.49
146_E151_G0.5320.49
88_K109_H0.5310.48
323_L360_F0.5310.48
130_V134_E0.5310.48
15_L19_L0.5310.48
22_A26_L0.5300.48
185_A216_R0.5280.48
399_K433_K0.5280.48
176_L388_Q0.5270.48
189_W211_A0.5270.48
255_I422_D0.5270.48
191_T195_E0.5270.48
27_G286_W0.5250.48
141_K151_G0.5250.48
121_I221_F0.5250.48
163_L166_L0.5240.48
107_L121_I0.5230.47
56_P65_N0.5220.47
295_K413_S0.5200.47
6_Q9_Q0.5200.47
415_R419_K0.5190.47
341_R415_R0.5190.47
399_K406_E0.5190.47
17_Q41_S0.5180.47
303_N331_C0.5180.47
300_R357_M0.5180.47
116_Y346_K0.5180.47
381_H410_I0.5180.47
343_I365_A0.5170.47
53_D400_L0.5170.47
243_I310_K0.5170.47
305_L328_V0.5170.47
193_S199_P0.5160.47
375_N379_K0.5160.47
27_G253_P0.5160.47
16_T22_A0.5150.46
385_L396_S0.5150.46
111_L365_A0.5150.46
120_D154_S0.5140.46
108_I424_M0.5130.46
156_Q406_E0.5130.46
26_L33_L0.5130.46
4_K349_Q0.5120.46
188_K412_I0.5120.46
95_N141_K0.5120.46
359_L362_S0.5110.46
43_E283_E0.5110.46
24_T36_Y0.5100.46
348_I355_F0.5090.46
397_D421_R0.5090.46
178_S201_H0.5090.46
265_L379_K0.5080.46
207_S211_A0.5080.46
109_H284_W0.5070.45
111_L372_D0.5060.45
280_K320_M0.5060.45
397_D415_R0.5040.45
158_C185_A0.5040.45
243_I413_S0.5030.45
176_L369_G0.5030.45
28_Y47_I0.5020.45
414_R419_K0.5020.45
297_T346_K0.5020.45
333_S399_K0.5010.45
29_H433_K0.5010.45
12_K289_R0.5000.45
69_A422_D0.5000.45
338_T415_R0.5000.45
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  
2k9mA 1 0.2982 100 0.745 Contact Map
2ahqA 1 0.1537 99.9 0.802 Contact Map
2k9lA 1 0.1743 99.6 0.878 Contact Map
1k78A 1 0.2729 96.4 0.949 Contact Map
1jyeA 2 0.0665 96.3 0.949 Contact Map
1zs4A 4 0.1835 96.2 0.95 Contact Map
3dbiA 2 0.0688 96.1 0.95 Contact Map
1qpzA 2 0.2271 95.9 0.951 Contact Map
1uxcA 1 0.1009 95.9 0.951 Contact Map
1pdnC 1 0.2706 95.8 0.951 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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