GREMLIN Database
RP54 - RNA polymerase sigma-54 factor
UniProt: P24255 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10898
Length: 477 (455)
Sequences: 2147 (1527)
Seq/√Len: 71.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
276_V344_S4.1031.00
423_L449_Q3.9621.00
424_V442_L3.6461.00
188_V205_Q3.5171.00
346_C370_I3.4311.00
236_M243_E3.4231.00
136_T174_E3.3451.00
159_E172_I3.2501.00
342_R374_V3.2471.00
366_V369_D3.2301.00
278_V390_L3.2131.00
280_K356_E3.1901.00
144_I182_I3.1611.00
141_A182_I3.0361.00
193_K197_D3.0351.00
158_L179_L3.0341.00
137_D178_V2.8321.00
192_A201_I2.8241.00
134_S137_D2.7471.00
219_I249_A2.7331.00
344_S390_L2.7221.00
346_C373_A2.6411.00
137_D177_A2.5881.00
148_V191_A2.5561.00
179_L193_K2.5321.00
257_D262_Q2.5231.00
285_W356_E2.4391.00
149_D155_T2.4281.00
257_D263_S2.4131.00
141_A178_V2.4071.00
140_I175_V2.4071.00
182_I191_A2.3561.00
218_L222_D2.3561.00
172_I176_E2.3071.00
204_S217_R2.2961.00
376_M381_I2.2871.00
374_V381_I2.2391.00
354_F397_F2.2381.00
140_I178_V2.2171.00
128_V141_A2.2081.00
397_F401_Y2.2011.00
128_V145_V2.1881.00
148_V182_I2.1611.00
179_L183_Q2.1441.00
346_C349_E2.1391.00
424_V446_L2.1301.00
188_V201_I2.1271.00
236_M246_L2.1191.00
124_L145_V2.0971.00
445_L448_E2.0921.00
350_Q365_M2.0661.00
183_Q193_K2.0341.00
200_L217_R2.0321.00
123_Y264_I2.0301.00
440_S444_S2.0281.00
201_I204_S2.0111.00
137_D174_E1.9971.00
428_I465_L1.9811.00
287_V348_V1.9811.00
242_K245_V1.9751.00
312_N315_D1.9741.00
352_Q356_E1.9711.00
223_H239_T1.9681.00
272_V389_Y1.9561.00
252_L255_S1.9361.00
427_L445_L1.9231.00
426_K430_A1.9211.00
137_D181_R1.9131.00
158_L175_V1.8861.00
427_L442_L1.8851.00
226_L231_D1.8601.00
153_Y198_C1.8551.00
125_M142_T1.8441.00
281_H284_H1.8201.00
118_Q126_W1.8121.00
235_L246_L1.8061.00
226_L235_L1.7991.00
128_V185_F1.7921.00
48_E300_N1.7781.00
425_K429_A1.7601.00
145_V185_F1.7431.00
151_T155_T1.7171.00
176_E193_K1.6861.00
350_Q373_A1.6771.00
131_T185_F1.6701.00
206_F252_L1.6561.00
179_L201_I1.6531.00
241_L249_A1.6440.99
140_I170_I1.6430.99
357_Q361_Y1.6340.99
223_H226_L1.6330.99
144_I191_A1.6290.99
441_K445_L1.6270.99
85_D92_Y1.6140.99
447_S452_M1.5920.99
354_F402_F1.5870.99
195_L259_R1.5830.99
162_L175_V1.5810.99
203_L220_I1.5760.99
161_I175_V1.5760.99
220_I224_L1.5740.99
367_L400_K1.5510.99
276_V390_L1.5410.99
195_L198_C1.5340.99
157_P160_D1.5270.99
196_R200_L1.5150.99
13_L16_T1.5130.99
198_C261_G1.5050.99
200_L221_S1.5010.99
367_L385_T1.5000.99
40_A325_D1.4850.99
342_R376_M1.4840.99
87_S91_I1.4810.99
355_F393_P1.4690.99
397_F402_F1.4690.99
201_I205_Q1.4680.99
398_E401_Y1.4670.99
203_L256_L1.4670.99
213_L217_R1.4610.99
297_L330_I1.4590.99
278_V348_V1.4590.99
153_Y259_R1.4550.99
153_Y195_L1.4530.99
15_M22_A1.4510.99
355_F392_S1.4480.99
280_K285_W1.4440.99
247_K475_Q1.4410.99
349_E373_A1.4340.99
141_A144_I1.4320.99
223_H238_V1.4280.99
224_L228_A1.4190.98
289_L341_L1.4120.98
86_A91_I1.4100.98
123_Y186_D1.4010.98
404_S416_S1.3940.98
199_L256_L1.3890.98
183_Q201_I1.3840.98
183_Q197_D1.3710.98
158_L176_E1.3640.98
196_R221_S1.3490.98
84_L87_S1.3400.98
279_R288_E1.3280.98
158_L172_I1.3250.98
196_R224_L1.3150.98
390_L393_P1.3060.97
94_A97_P1.3020.97
360_E426_K1.2920.97
226_L234_T1.2920.97
141_A185_F1.2900.97
244_D247_K1.2830.97
224_L227_L1.2740.97
241_L246_L1.2740.97
200_L204_S1.2680.97
345_R349_E1.2680.97
409_T412_G1.2620.97
389_Y398_E1.2510.97
348_V355_F1.2500.97
350_Q370_I1.2460.97
347_I365_M1.2440.97
365_M369_D1.2310.96
247_K251_N1.2170.96
203_L252_L1.2140.96
124_L190_V1.2070.96
405_S417_S1.2040.96
198_C259_R1.2000.96
435_K441_K1.1990.96
140_I174_E1.1930.96
80_E83_P1.1780.95
226_L238_V1.1610.95
232_F246_L1.1570.95
350_Q369_D1.1500.95
420_I446_L1.1460.94
441_K444_S1.1460.94
353_A363_K1.1410.94
84_L92_Y1.1390.94
176_E180_K1.1340.94
16_T23_I1.1280.94
144_I161_I1.1270.94
144_I179_L1.1180.94
344_S399_L1.1170.94
299_I330_I1.1090.93
212_W249_A1.1050.93
15_M23_I1.0990.93
151_T259_R1.0930.93
192_A198_C1.0930.93
144_I175_V1.0890.93
443_T447_S1.0880.93
354_F401_Y1.0830.93
120_L264_I1.0820.93
178_V191_A1.0800.93
41_L47_L1.0780.92
121_Q146_D1.0700.92
171_D174_E1.0660.92
182_I201_I1.0650.92
328_W335_S1.0650.92
346_C350_Q1.0620.92
41_L49_Q1.0610.92
84_L91_I1.0600.92
133_F181_R1.0600.92
217_R221_S1.0560.92
86_A89_D1.0540.92
251_N475_Q1.0500.91
153_Y303_Y1.0490.91
277_L391_H1.0390.91
121_Q150_E1.0380.91
141_A191_A1.0220.90
428_I467_I1.0210.90
390_L399_L1.0160.90
36_E40_A1.0150.90
38_Q42_E1.0120.90
331_K378_E1.0090.90
219_I253_I1.0030.89
193_K201_I1.0000.89
299_I326_A0.9960.89
432_N435_K0.9880.89
76_K80_E0.9880.89
87_S92_Y0.9850.89
83_P87_S0.9850.89
45_P318_F0.9810.88
174_E177_A0.9770.88
437_L442_L0.9760.88
208_K213_L0.9700.88
329_L470_S0.9700.88
446_L458_V0.9690.88
123_Y126_W0.9680.88
86_A90_T0.9670.88
212_W241_L0.9660.88
179_L192_A0.9620.87
422_A425_K0.9580.87
392_S395_G0.9530.87
313_D316_S0.9490.87
60_E64_S0.9490.87
409_T415_A0.9430.86
421_R464_S0.9410.86
445_L449_Q0.9400.86
84_L88_W0.9390.86
280_K283_G0.9290.85
431_E436_P0.9270.85
433_P475_Q0.9240.85
120_L123_Y0.9230.85
13_L19_L0.9190.85
342_R345_R0.9170.85
18_Q463_E0.9170.85
285_W355_F0.9160.85
20_Q24_R0.9130.84
344_S348_V0.9120.84
147_A156_V0.9090.84
427_L437_L0.9070.84
284_H352_Q0.9070.84
6_Q12_Q0.9070.84
231_D234_T0.9060.84
281_H286_T0.8980.83
426_K449_Q0.8970.83
82_L87_S0.8960.83
331_K370_I0.8900.83
368_A378_E0.8890.83
127_Q187_P0.8890.83
232_F250_V0.8890.83
128_V133_F0.8870.83
53_H442_L0.8860.83
87_S94_A0.8860.83
41_L52_T0.8840.83
40_A329_L0.8840.83
323_L327_K0.8810.82
372_Q375_E0.8800.82
162_L170_I0.8720.82
297_L333_L0.8700.82
343_V398_E0.8670.81
340_L384_V0.8650.81
85_D90_T0.8640.81
119_T122_D0.8630.81
235_L238_V0.8600.81
243_E247_K0.8590.81
444_S447_S0.8590.81
198_C257_D0.8560.80
348_V390_L0.8480.80
165_I170_I0.8470.80
181_R184_R0.8410.79
129_E138_R0.8400.79
124_L185_F0.8400.79
39_Q43_S0.8390.79
143_S161_I0.8390.79
331_K377_H0.8390.79
143_S164_S0.8380.79
249_A298_Q0.8360.79
156_V160_D0.8350.79
353_A361_Y0.8340.79
20_Q29_S0.8330.79
128_V132_P0.8330.79
29_S387_Q0.8320.79
37_L41_L0.8300.78
59_R62_Q0.8300.78
178_V181_R0.8290.78
343_V367_L0.8260.78
338_D342_R0.8240.78
184_R201_I0.8240.78
291_S337_N0.8240.78
82_L88_W0.8180.77
407_V422_A0.8150.77
78_M82_L0.8120.77
276_V399_L0.8090.77
193_K198_C0.8060.76
359_E394_R0.8050.76
227_L232_F0.8050.76
206_F209_T0.8030.76
398_E402_F0.8030.76
277_L293_S0.8000.76
120_L261_G0.8000.76
210_T252_L0.7980.76
310_A314_G0.7930.75
432_N436_P0.7920.75
227_L230_H0.7920.75
229_N472_Q0.7910.75
359_E401_Y0.7910.75
89_D92_Y0.7870.75
88_W92_Y0.7860.74
261_G402_F0.7840.74
454_A457_T0.7810.74
196_R225_D0.7800.74
141_A145_V0.7790.74
235_L241_L0.7790.74
299_I323_L0.7790.74
346_C374_V0.7780.74
277_L290_N0.7770.74
16_T19_L0.7730.73
459_A463_E0.7680.73
369_D372_Q0.7680.73
25_L384_V0.7640.72
366_V405_S0.7630.72
18_Q25_L0.7630.72
55_E60_E0.7620.72
213_L249_A0.7590.72
407_V420_I0.7580.72
153_Y193_K0.7570.72
15_M472_Q0.7560.72
121_Q148_V0.7550.71
83_P88_W0.7550.71
179_L191_A0.7550.71
285_W393_P0.7530.71
335_S340_L0.7530.71
18_Q24_R0.7520.71
323_L326_A0.7510.71
20_Q391_H0.7500.71
257_D261_G0.7500.71
246_L250_V0.7490.71
96_T99_G0.7490.71
54_E61_T0.7460.71
175_V178_V0.7460.71
443_T453_V0.7450.70
140_I165_I0.7410.70
442_L458_V0.7400.70
401_Y418_T0.7390.70
334_E337_N0.7380.70
367_L392_S0.7380.70
385_T400_K0.7370.70
223_H235_L0.7370.70
172_I428_I0.7370.70
79_P82_L0.7360.70
404_S418_T0.7360.70
390_L397_F0.7340.69
184_R205_Q0.7340.69
13_L23_I0.7320.69
453_V458_V0.7310.69
227_L394_R0.7310.69
276_V287_V0.7280.69
200_L220_I0.7280.69
143_S147_A0.7280.69
85_D91_I0.7270.69
58_T61_T0.7250.68
419_A451_I0.7250.68
88_W91_I0.7240.68
118_Q123_Y0.7220.68
108_E113_Q0.7220.68
276_V340_L0.7220.68
55_E58_T0.7210.68
409_T420_I0.7210.68
109_L113_Q0.7210.68
340_L398_E0.7200.68
347_I402_F0.7200.68
328_W332_S0.7190.68
181_R191_A0.7160.67
109_L112_Y0.7160.67
299_I304_A0.7150.67
89_D93_T0.7130.67
54_E57_D0.7110.67
287_V344_S0.7110.67
110_P114_G0.7090.67
470_S475_Q0.7090.67
425_K465_L0.7080.67
58_T63_D0.7040.66
334_E338_D0.7030.66
368_A372_Q0.7000.66
386_T400_K0.7000.66
227_L253_I0.7000.66
83_P86_A0.6990.66
210_T213_L0.6980.65
243_E246_L0.6960.65
391_H396_I0.6950.65
209_T252_L0.6930.65
355_F401_Y0.6900.65
430_A437_L0.6900.65
332_S340_L0.6890.64
182_I185_F0.6880.64
20_Q378_E0.6880.64
28_L438_S0.6870.64
6_Q10_S0.6870.64
184_R204_S0.6860.64
24_R36_E0.6850.64
250_V474_K0.6840.64
230_H254_Q0.6800.63
133_F137_D0.6790.63
297_L463_E0.6790.63
362_M384_V0.6770.63
410_E447_S0.6770.63
183_Q261_G0.6770.63
341_L345_R0.6760.63
385_T403_F0.6740.63
328_W384_V0.6730.63
427_L438_S0.6730.63
78_M81_E0.6710.62
52_T62_Q0.6700.62
387_Q398_E0.6700.62
4_G24_R0.6690.62
357_Q363_K0.6690.62
19_L22_A0.6690.62
106_D428_I0.6680.62
153_Y261_G0.6670.62
14_A17_P0.6670.62
363_K398_E0.6670.62
12_Q39_Q0.6650.62
442_L445_L0.6640.62
302_H306_M0.6620.61
343_V347_I0.6610.61
15_M19_L0.6600.61
328_W376_M0.6570.61
279_R286_T0.6570.61
127_Q185_F0.6550.61
437_L445_L0.6550.61
339_T384_V0.6550.61
86_A92_Y0.6470.60
459_A471_N0.6450.59
38_Q49_Q0.6440.59
355_F394_R0.6440.59
59_R173_D0.6430.59
93_T96_T0.6430.59
101_S104_Y0.6410.59
37_L391_H0.6400.59
245_V248_E0.6400.59
63_D76_K0.6380.59
232_F376_M0.6360.58
407_V414_E0.6360.58
27_Q203_L0.6350.58
85_D88_W0.6310.58
60_E65_E0.6310.58
28_L36_E0.6280.57
365_M405_S0.6270.57
133_F178_V0.6260.57
109_L114_G0.6250.57
131_T181_R0.6250.57
384_V454_A0.6230.57
165_I175_V0.6230.57
292_D334_E0.6220.57
147_A310_A0.6210.57
209_T217_R0.6210.57
54_E60_E0.6190.56
343_V370_I0.6190.56
144_I158_L0.6170.56
441_K448_E0.6160.56
22_A26_L0.6150.56
19_L378_E0.6130.56
337_N454_A0.6130.56
23_I328_W0.6130.56
332_S469_P0.6120.55
56_I60_E0.6120.55
14_A20_Q0.6120.55
253_I370_I0.6110.55
162_L172_I0.6110.55
20_Q28_L0.6110.55
365_M404_S0.6100.55
19_L23_I0.6090.55
6_Q9_L0.6060.55
177_A180_K0.6050.55
265_Q268_E0.6050.55
194_D222_D0.6040.54
423_L426_K0.6030.54
354_F398_E0.6010.54
350_Q363_K0.6010.54
261_G354_F0.6000.54
156_V164_S0.5990.54
153_Y257_D0.5990.54
179_L182_I0.5990.54
117_T268_E0.5980.54
137_D176_E0.5980.54
290_N295_P0.5970.54
285_W394_R0.5960.53
19_L377_H0.5950.53
235_L239_T0.5940.53
373_A421_R0.5940.53
366_V459_A0.5940.53
52_T58_T0.5940.53
218_L223_H0.5910.53
127_Q399_L0.5910.53
121_Q125_M0.5890.53
385_T398_E0.5890.53
271_Y396_I0.5880.52
290_N363_K0.5880.52
441_K474_K0.5880.52
157_P193_K0.5880.52
155_T194_D0.5870.52
165_I248_E0.5870.52
170_I175_V0.5860.52
92_Y96_T0.5860.52
213_L253_I0.5850.52
23_I26_L0.5840.52
305_S308_N0.5840.52
143_S165_I0.5840.52
420_I453_V0.5840.52
179_L197_D0.5840.52
287_V345_R0.5830.52
164_S465_L0.5830.52
342_R399_L0.5810.52
367_L379_S0.5810.52
25_L376_M0.5810.52
55_E64_S0.5800.52
396_I469_P0.5800.52
86_A93_T0.5790.51
234_T376_M0.5780.51
31_L51_D0.5780.51
375_E428_I0.5770.51
207_D210_T0.5760.51
24_R37_L0.5750.51
133_F186_D0.5740.51
456_R460_K0.5730.51
225_D229_N0.5710.50
285_W348_V0.5710.50
219_I239_T0.5710.50
224_L250_V0.5710.50
61_T312_N0.5700.50
455_R461_Y0.5690.50
20_Q331_K0.5690.50
46_L323_L0.5690.50
18_Q454_A0.5680.50
328_W407_V0.5680.50
138_R458_V0.5670.50
61_T83_P0.5640.50
125_M145_V0.5640.50
22_A30_T0.5640.50
28_L47_L0.5630.49
243_E381_I0.5610.49
25_L386_T0.5600.49
112_Y115_E0.5600.49
55_E435_K0.5580.49
384_V421_R0.5580.49
81_E90_T0.5570.49
249_A253_I0.5570.49
24_R278_V0.5560.49
135_D180_K0.5560.49
146_D231_D0.5550.48
340_L343_V0.5550.48
29_S32_E0.5550.48
362_M418_T0.5530.48
162_L363_K0.5530.48
153_Y258_P0.5520.48
113_Q472_Q0.5520.48
134_S178_V0.5520.48
135_D138_R0.5510.48
81_E89_D0.5510.48
83_P91_I0.5510.48
57_D61_T0.5510.48
276_V300_N0.5510.48
206_F210_T0.5510.48
180_K204_S0.5500.48
28_L400_K0.5490.48
458_V463_E0.5490.48
424_V452_M0.5490.48
412_G463_E0.5480.48
469_P472_Q0.5480.48
137_D140_I0.5480.48
170_I174_E0.5480.48
121_Q261_G0.5440.47
222_D248_E0.5440.47
60_E63_D0.5430.47
41_L297_L0.5430.47
131_T381_I0.5430.47
457_T460_K0.5420.47
378_E459_A0.5420.47
370_I374_V0.5420.47
61_T64_S0.5410.47
227_L464_S0.5410.47
207_D213_L0.5400.47
456_R461_Y0.5400.47
198_C201_I0.5400.47
203_L210_T0.5400.47
111_V406_H0.5390.46
203_L206_F0.5390.46
268_E363_K0.5390.46
161_I289_L0.5380.46
176_E179_L0.5380.46
194_D331_K0.5370.46
85_D93_T0.5370.46
57_D60_E0.5370.46
242_K246_L0.5350.46
20_Q377_H0.5350.46
408_N421_R0.5350.46
79_P88_W0.5350.46
438_S441_K0.5350.46
106_D420_I0.5350.46
219_I246_L0.5340.46
410_E450_G0.5340.46
347_I398_E0.5340.46
81_E85_D0.5330.46
37_L43_S0.5310.46
158_L193_K0.5300.45
106_D463_E0.5300.45
378_E417_S0.5300.45
94_A98_S0.5300.45
442_L451_I0.5300.45
8_R324_Q0.5300.45
385_T399_L0.5300.45
82_L92_Y0.5290.45
353_A430_A0.5290.45
307_C315_D0.5280.45
87_S93_T0.5280.45
297_L465_L0.5280.45
43_S322_N0.5270.45
157_P161_I0.5270.45
32_E36_E0.5260.45
353_A357_Q0.5260.45
124_L389_Y0.5250.45
287_V341_L0.5250.45
228_A259_R0.5250.45
175_V179_L0.5240.45
345_R452_M0.5230.45
407_V449_Q0.5230.45
102_G107_D0.5220.44
29_S36_E0.5220.44
178_V182_I0.5220.44
244_D341_L0.5200.44
99_G102_G0.5200.44
23_I417_S0.5200.44
435_K471_N0.5190.44
282_N308_N0.5190.44
314_G317_Q0.5180.44
172_I266_T0.5170.44
209_T221_S0.5160.44
39_Q53_H0.5150.44
145_V182_I0.5140.43
57_D62_Q0.5140.43
141_A326_A0.5140.43
46_L253_I0.5130.43
208_K252_L0.5130.43
158_L174_E0.5120.43
34_Q37_L0.5120.43
468_P472_Q0.5120.43
54_E62_Q0.5120.43
285_W454_A0.5110.43
80_E84_L0.5110.43
85_D89_D0.5100.43
291_S294_I0.5100.43
156_V161_I0.5100.43
28_L387_Q0.5100.43
154_L161_I0.5090.43
173_D428_I0.5090.43
123_Y190_V0.5080.43
261_G328_W0.5080.43
232_F243_E0.5070.43
16_T20_Q0.5060.42
34_Q49_Q0.5050.42
42_E381_I0.5040.42
195_L442_L0.5040.42
37_L40_A0.5040.42
15_M475_Q0.5040.42
310_A315_D0.5030.42
79_P84_L0.5020.42
392_S400_K0.5020.42
242_K255_S0.5020.42
35_Q39_Q0.5020.42
102_G106_D0.5020.42
304_A390_L0.5020.42
401_Y404_S0.5010.42
76_K83_P0.5010.42
37_L49_Q0.5000.42
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 0.2725 100 0.763 Contact Map
2ahqA 1 0.1405 100 0.816 Contact Map
2k9lA 1 0.1593 99.7 0.886 Contact Map
1jyeA 2 0.044 96.9 0.952 Contact Map
1qpzA 2 0.1761 96.8 0.953 Contact Map
3dbiA 2 0.0608 96.6 0.955 Contact Map
1k78A 1 0.2495 96.4 0.955 Contact Map
1zs4A 4 0.174 96.2 0.956 Contact Map
1pdnC 1 0.2474 96 0.957 Contact Map
1uxcA 1 0.0964 96 0.957 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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