GREMLIN Database
Q980R0 - DNA-directed RNA polymerase, subunit B'' (RpoB2)
UniProt: Q980R0 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 480 (416)
Sequences: 2340 (1160)
Seq/√Len: 56.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
25_R29_D6.3591.00
223_F319_I6.0711.00
40_Q60_L4.9391.00
66_G95_P4.6791.00
309_K321_K4.6061.00
40_Q62_K4.6041.00
264_N267_D4.2951.00
31_Y121_I4.1381.00
40_Q44_D4.1341.00
210_F323_I3.9261.00
94_A121_I3.6741.00
64_R113_E3.6701.00
59_R101_I3.6491.00
50_P57_K3.4491.00
62_K99_T3.2301.00
429_V453_M3.1471.00
265_V290_Q3.0851.00
60_L362_V2.9501.00
266_D286_I2.8851.00
84_E88_R2.8601.00
159_R411_S2.8531.00
32_N36_R2.7601.00
57_K103_V2.7331.00
300_H478_C2.7261.00
30_S347_G2.6371.00
424_S469_N2.6251.00
236_R240_Y2.5941.00
33_D37_N2.5491.00
262_I268_A2.5461.00
324_E330_R2.5251.00
232_I241_A2.5091.00
311_K314_Y2.4711.00
101_I111_P2.3221.00
265_V269_L2.2821.00
228_R235_D2.2131.00
202_I318_A2.2101.00
241_A316_A2.2021.00
251_E255_S2.0821.00
47_G100_M2.0621.00
324_E329_R2.0341.00
251_E254_P2.0291.00
64_R97_W2.0161.00
271_F274_S1.9861.00
61_G101_I1.9841.00
28_L32_N1.9651.00
99_T113_E1.9301.00
221_I371_K1.9211.00
412_Q446_H1.9181.00
250_N254_P1.8781.00
39_L63_I1.8581.00
269_L290_Q1.8210.99
227_M232_I1.7440.99
33_D38_K1.7200.99
41_E44_D1.7180.99
422_M426_L1.7150.99
457_E469_N1.7010.99
424_S457_E1.7010.99
35_V121_I1.6910.99
325_L332_P1.6820.99
227_M316_A1.6480.99
97_W113_E1.6420.99
66_G94_A1.6370.99
384_L453_M1.6240.99
248_V251_E1.5960.98
66_G97_W1.5830.98
69_R119_L1.5750.98
99_T111_P1.5640.98
457_E460_E1.5490.98
25_R475_S1.5360.98
50_P54_P1.5310.98
210_F223_F1.5240.98
431_S449_Q1.5210.98
341_K403_W1.5160.98
291_Q295_K1.5130.98
250_N253_F1.5040.98
71_R85_A1.4950.98
273_G289_A1.4740.97
82_P149_G1.4730.97
445_L464_S1.4650.97
426_L457_E1.4600.97
226_L315_L1.4400.97
321_K330_R1.4370.97
295_K299_P1.4210.97
39_L354_F1.4120.97
323_I327_L1.4080.97
227_M319_I1.4070.97
252_L255_S1.3930.96
252_L256_L1.3920.96
428_R457_E1.3820.96
200_V212_V1.3820.96
30_S158_E1.3820.96
349_L423_L1.3810.96
412_Q425_H1.3810.96
212_V226_L1.3790.96
22_G28_L1.3780.96
413_L422_M1.3770.96
251_E256_L1.3610.96
232_I238_I1.3570.96
396_H403_W1.3570.96
223_F315_L1.3510.96
172_V187_A1.3460.96
414_L426_L1.3440.96
200_V204_R1.3430.96
228_R261_S1.3410.96
98_L116_I1.3220.95
202_I322_V1.3100.95
270_D274_S1.2930.95
165_E397_A1.2920.95
334_D446_H1.2870.94
184_T208_G1.2780.94
250_N258_Q1.2730.94
38_K351_A1.2660.94
253_F257_E1.2640.94
95_P117_G1.2560.94
165_E468_K1.2510.94
452_R463_N1.2420.93
238_I319_I1.2290.93
388_D423_L1.2270.93
41_E351_A1.2230.93
203_E213_S1.2220.93
42_I45_E1.2150.92
149_G174_V1.2130.92
82_P92_Y1.2110.92
39_L62_K1.2090.92
218_P276_V1.2080.92
159_R406_G1.2080.92
412_Q428_R1.2030.92
191_S195_G1.1980.92
443_R454_C1.1920.92
443_R465_G1.1910.92
461_G465_G1.1840.91
221_I226_L1.1840.91
175_D183_I1.1830.91
323_I326_Y1.1830.91
82_P153_I1.1800.91
343_L476_N1.1790.91
65_I96_L1.1760.91
171_R318_A1.1710.91
394_I398_L1.1660.91
189_I202_I1.1630.91
189_I318_A1.1620.91
29_D32_N1.1600.91
151_Y400_T1.1470.90
60_L358_F1.1460.90
238_I242_V1.1430.90
58_V389_I1.1410.90
61_G99_T1.1410.90
163_T343_L1.1320.90
428_R460_E1.1270.89
101_I109_A1.1220.89
36_R154_V1.1220.89
249_Q255_S1.1190.89
367_Y371_K1.1180.89
454_C458_T1.1150.89
96_L119_L1.1060.88
24_V423_L1.1050.88
241_A320_S1.1030.88
406_G469_N1.1020.88
450_W464_S1.1010.88
58_V102_P1.0960.88
34_F397_A1.0940.88
42_I351_A1.0900.88
269_L286_I1.0900.88
460_E467_V1.0880.88
335_K341_K1.0850.87
286_I290_Q1.0830.87
433_L442_A1.0810.87
210_F275_R1.0800.87
182_N208_G1.0710.87
254_P260_S1.0620.86
455_P458_T1.0580.86
341_K439_N1.0550.86
435_R463_N1.0540.86
237_D240_Y1.0520.86
406_G457_E1.0490.86
82_P86_R1.0480.86
341_K428_R1.0470.86
440_F444_D1.0420.85
86_R149_G1.0390.85
82_P161_I1.0330.85
29_D33_D1.0290.84
246_P253_F1.0280.84
97_W115_Y1.0180.84
167_L432_S1.0160.84
415_D422_M1.0120.83
254_P257_E1.0080.83
242_V252_L0.9950.82
239_V253_F0.9920.82
209_T222_P0.9910.82
444_D452_R0.9890.82
200_V315_L0.9870.82
191_S194_A0.9850.82
425_H463_N0.9830.82
435_R457_E0.9760.81
385_V389_I0.9760.81
59_R103_V0.9720.81
446_H460_E0.9700.81
47_G59_R0.9650.80
158_E228_R0.9640.80
234_T237_D0.9600.80
149_G398_L0.9600.80
101_I113_E0.9540.80
93_A118_D0.9510.79
454_C461_G0.9500.79
428_R449_Q0.9440.79
161_I411_S0.9420.79
97_W476_N0.9410.79
95_P118_D0.9370.78
446_H449_Q0.9360.78
45_E351_A0.9350.78
306_E311_K0.9330.78
412_Q457_E0.9300.78
115_Y118_D0.9280.78
37_N41_E0.9270.78
235_D264_N0.9250.78
381_L385_V0.9120.77
247_E251_E0.9070.76
162_V433_L0.9060.76
179_T315_L0.9050.76
63_I96_L0.9040.76
211_H448_T0.9030.76
234_T238_I0.9020.76
33_D351_A0.9010.76
402_N413_L0.9010.76
381_L384_L0.9000.76
362_V366_T0.9000.76
122_M150_G0.8960.75
12_R15_E0.8950.75
33_D41_E0.8910.75
256_L260_S0.8900.75
249_Q257_E0.8890.75
211_H220_K0.8890.75
160_V428_R0.8880.75
432_S438_P0.8850.74
270_D286_I0.8800.74
86_R158_E0.8800.74
42_I46_Q0.8780.74
418_N456_F0.8770.74
104_E107_I0.8770.74
153_I295_K0.8710.73
414_L421_S0.8710.73
119_L327_L0.8680.73
300_H311_K0.8670.73
251_E326_Y0.8660.73
253_F256_L0.8660.73
455_P459_P0.8640.73
86_R275_R0.8580.72
225_I262_I0.8540.72
279_G289_A0.8520.72
412_Q460_E0.8520.72
235_D262_I0.8510.71
232_I312_A0.8490.71
32_N42_I0.8470.71
158_E347_G0.8470.71
185_H322_V0.8440.71
417_T453_M0.8430.71
194_A404_V0.8370.70
228_R262_I0.8350.70
416_R422_M0.8340.70
443_R461_G0.8330.70
204_R221_I0.8330.70
396_H399_A0.8320.70
382_K386_R0.8300.70
22_G26_Q0.8270.69
117_G425_H0.8270.69
96_L216_A0.8260.69
438_P442_A0.8250.69
182_N187_A0.8230.69
268_A428_R0.8210.69
418_N427_R0.8190.69
26_Q470_L0.8180.68
89_N353_L0.8150.68
245_D327_L0.8130.68
47_G51_T0.8130.68
29_D478_C0.8130.68
98_L390_V0.8130.68
433_L438_P0.8120.68
320_S329_R0.8120.68
398_L401_G0.8080.67
161_I346_A0.8070.67
269_L292_I0.8070.67
348_D404_V0.8070.67
82_P311_K0.8040.67
413_L416_R0.8010.67
241_A313_Y0.8010.67
88_R347_G0.7980.66
365_L387_P0.7900.66
22_G25_R0.7890.66
361_F369_L0.7890.66
32_N103_V0.7880.66
229_A268_A0.7880.66
448_T457_E0.7870.65
13_V151_Y0.7870.65
249_Q253_F0.7860.65
45_E355_R0.7860.65
334_D342_R0.7830.65
212_V223_F0.7820.65
415_D421_S0.7800.65
58_V160_V0.7800.65
86_R423_L0.7780.65
178_K247_E0.7770.64
154_V163_T0.7770.64
66_G263_A0.7740.64
227_M315_L0.7720.64
434_A463_N0.7720.64
385_V388_D0.7710.64
183_I206_K0.7710.64
443_R458_T0.7710.64
160_V412_Q0.7700.64
433_L441_E0.7680.64
248_V255_S0.7660.63
64_R301_L0.7650.63
452_R456_F0.7650.63
255_S260_S0.7620.63
396_H400_T0.7590.63
120_P156_G0.7590.63
91_T154_V0.7590.63
193_T341_K0.7570.62
98_L358_F0.7560.62
290_Q398_L0.7560.62
415_D418_N0.7550.62
410_V432_S0.7550.62
325_L330_R0.7530.62
358_F423_L0.7530.62
431_S457_E0.7520.62
458_T465_G0.7510.62
180_G184_T0.7510.62
43_I63_I0.7480.61
186_T238_I0.7440.61
119_L394_I0.7430.61
364_D368_Q0.7410.61
221_I272_I0.7400.61
321_K324_E0.7390.61
175_D178_K0.7380.60
316_A320_S0.7370.60
433_L440_F0.7340.60
224_V256_L0.7330.60
227_M242_V0.7310.60
155_N395_R0.7300.60
225_I318_A0.7290.59
203_E403_W0.7290.59
250_N256_L0.7290.59
188_K218_P0.7280.59
225_I271_F0.7280.59
201_T204_R0.7270.59
65_I94_A0.7270.59
250_N255_S0.7260.59
307_D310_K0.7240.59
12_R16_A0.7240.59
34_F350_F0.7220.59
416_R436_G0.7210.59
427_R446_H0.7210.59
446_H457_E0.7210.59
52_E366_T0.7190.58
322_V326_Y0.7190.58
213_S275_R0.7180.58
243_S429_V0.7170.58
15_E65_I0.7170.58
43_I116_I0.7140.58
203_E471_A0.7120.58
57_K105_N0.7110.58
44_D83_M0.7100.57
14_I24_V0.7080.57
204_R326_Y0.7060.57
250_N257_E0.7030.57
122_M474_G0.7020.57
112_E387_P0.7020.57
63_I116_I0.7000.56
369_L476_N0.6990.56
205_L211_H0.6990.56
276_V293_I0.6970.56
440_F463_N0.6970.56
406_G431_S0.6930.56
236_R242_V0.6910.55
248_V253_F0.6870.55
345_L476_N0.6870.55
28_L311_K0.6830.55
451_G465_G0.6830.55
400_T403_W0.6820.54
249_Q256_L0.6820.54
354_F401_G0.6800.54
397_A448_T0.6800.54
202_I341_K0.6800.54
36_R121_I0.6780.54
315_L319_I0.6780.54
65_I236_R0.6770.54
410_V416_R0.6760.54
338_Y422_M0.6760.54
59_R67_K0.6750.54
248_V258_Q0.6730.53
247_E254_P0.6730.53
214_F298_L0.6720.53
151_Y158_E0.6720.53
189_I238_I0.6710.53
158_E459_P0.6710.53
231_G238_I0.6710.53
177_G183_I0.6710.53
415_D426_L0.6710.53
103_V109_A0.6700.53
448_T460_E0.6680.53
454_C465_G0.6680.53
368_Q386_R0.6640.52
25_R37_N0.6630.52
202_I226_L0.6610.52
320_S324_E0.6600.52
441_E444_D0.6590.52
449_Q457_E0.6590.52
353_L356_V0.6580.52
216_A220_K0.6580.52
178_K182_N0.6580.52
24_V408_T0.6580.52
39_L52_E0.6560.52
16_A366_T0.6530.51
340_N420_L0.6530.51
222_P356_V0.6520.51
36_R41_E0.6520.51
230_L312_A0.6510.51
229_A240_Y0.6490.51
230_L315_L0.6490.51
89_N96_L0.6460.51
16_A315_L0.6460.51
412_Q458_T0.6440.50
100_M285_R0.6410.50
338_Y449_Q0.6410.50
85_A88_R0.6400.50
27_H433_L0.6400.50
456_F463_N0.6390.50
18_F402_N0.6390.50
361_F395_R0.6380.50
214_F272_I0.6370.50
202_I207_D0.6360.49
190_I194_A0.6350.49
442_A467_V0.6340.49
96_L115_Y0.6340.49
420_L423_L0.6320.49
53_I56_L0.6320.49
443_R460_E0.6320.49
431_S467_V0.6290.49
263_A267_D0.6280.49
236_R264_N0.6280.49
343_L453_M0.6270.48
48_E58_V0.6250.48
149_G409_G0.6240.48
189_I315_L0.6240.48
158_E339_A0.6220.48
27_H162_V0.6210.48
350_F401_G0.6210.48
262_I267_D0.6200.48
372_S382_K0.6190.48
14_I447_G0.6180.47
221_I315_L0.6170.47
31_Y299_P0.6160.47
65_I119_L0.6160.47
439_N469_N0.6160.47
293_I298_L0.6160.47
301_L307_D0.6150.47
89_N195_G0.6140.47
206_K345_L0.6130.47
424_S441_E0.6120.47
100_M385_V0.6120.47
45_E50_P0.6120.47
414_L442_A0.6100.47
340_N405_G0.6090.46
192_S195_G0.6090.46
119_L383_A0.6090.46
437_Q462_P0.6060.46
43_I53_I0.6060.46
272_I381_L0.6060.46
22_G35_V0.6050.46
285_R414_L0.6040.46
438_P444_D0.6040.46
58_V369_L0.6030.46
123_L170_N0.6030.46
454_C459_P0.6010.46
255_S262_I0.6010.46
432_S436_G0.6010.46
460_E469_N0.6000.45
441_E445_L0.5990.45
43_I367_Y0.5990.45
290_Q294_D0.5990.45
184_T293_I0.5990.45
412_Q422_M0.5990.45
406_G425_H0.5990.45
64_R99_T0.5960.45
151_Y346_A0.5960.45
202_I206_K0.5940.45
328_G331_E0.5940.45
178_K328_G0.5930.45
96_L354_F0.5930.45
249_Q252_L0.5910.45
46_Q355_R0.5890.44
68_P116_I0.5880.44
107_I388_D0.5880.44
67_K95_P0.5870.44
437_Q444_D0.5860.44
156_G461_G0.5860.44
413_L467_V0.5850.44
214_F297_F0.5850.44
278_I281_K0.5840.44
436_G439_N0.5840.44
225_I408_T0.5840.44
160_V449_Q0.5820.44
153_I354_F0.5800.43
184_T204_R0.5800.43
153_I265_V0.5800.43
51_T55_G0.5800.43
161_I251_E0.5790.43
349_L455_P0.5790.43
28_L296_Y0.5780.43
353_L397_A0.5780.43
332_P365_L0.5780.43
82_P121_I0.5770.43
35_V119_L0.5750.43
248_V252_L0.5750.43
213_S230_L0.5750.43
303_T314_Y0.5720.42
251_E260_S0.5720.42
33_D348_D0.5710.42
92_Y96_L0.5700.42
403_W410_V0.5680.42
92_Y120_P0.5680.42
425_H455_P0.5680.42
413_L426_L0.5670.42
420_L475_S0.5650.42
417_T476_N0.5640.42
241_A343_L0.5630.42
460_E465_G0.5620.41
114_V210_F0.5610.41
82_P150_G0.5590.41
46_Q358_F0.5580.41
425_H469_N0.5570.41
151_Y401_G0.5570.41
61_G343_L0.5560.41
63_I406_G0.5550.41
91_T264_N0.5530.40
341_K357_A0.5520.40
428_R435_R0.5510.40
397_A400_T0.5510.40
304_S447_G0.5490.40
415_D425_H0.5490.40
200_V350_F0.5490.40
370_E388_D0.5480.40
261_S269_L0.5470.40
403_W407_R0.5470.40
252_L319_I0.5470.40
104_E319_I0.5470.40
36_R40_Q0.5470.40
37_N40_Q0.5460.40
435_R440_F0.5450.40
100_M226_L0.5450.40
430_I467_V0.5440.40
445_L455_P0.5440.40
348_D452_R0.5440.40
19_K32_N0.5440.40
362_V402_N0.5420.39
397_A411_S0.5410.39
46_Q359_K0.5410.39
194_A419_W0.5400.39
360_A389_I0.5380.39
246_P315_L0.5380.39
63_I246_P0.5370.39
35_V44_D0.5360.39
116_I257_E0.5350.39
49_I60_L0.5330.38
55_G64_R0.5310.38
282_R363_K0.5300.38
23_L423_L0.5300.38
247_E261_S0.5300.38
354_F394_I0.5290.38
365_L384_L0.5290.38
165_E441_E0.5290.38
149_G235_D0.5280.38
420_L428_R0.5280.38
167_L170_N0.5280.38
68_P71_R0.5280.38
302_G333_D0.5280.38
22_G349_L0.5280.38
120_P152_F0.5270.38
470_L476_N0.5260.38
321_K325_L0.5260.38
82_P85_A0.5250.38
59_R109_A0.5240.37
333_D340_N0.5230.37
441_E457_E0.5220.37
360_A364_D0.5220.37
164_Q432_S0.5200.37
255_S258_Q0.5190.37
92_Y451_G0.5180.37
252_L323_I0.5170.37
42_I47_G0.5160.37
162_V427_R0.5160.37
164_Q430_I0.5160.37
248_V254_P0.5150.37
55_G274_S0.5150.37
434_A440_F0.5140.36
245_D257_E0.5140.36
388_D399_A0.5140.36
37_N44_D0.5140.36
58_V285_R0.5130.36
82_P106_N0.5120.36
27_H173_L0.5120.36
53_I119_L0.5110.36
21_K63_I0.5110.36
20_S25_R0.5110.36
463_N467_V0.5110.36
399_A402_N0.5100.36
90_L292_I0.5100.36
414_L472_V0.5100.36
172_V202_I0.5070.36
85_A339_A0.5070.36
20_S37_N0.5070.36
276_V296_Y0.5070.36
296_Y434_A0.5050.36
161_I383_A0.5050.36
196_Y348_D0.5040.35
39_L221_I0.5040.35
414_L422_M0.5030.35
188_K201_T0.5020.35
106_N266_D0.5020.35
179_T210_F0.5010.35
459_P465_G0.5010.35
32_N62_K0.5010.35
307_D323_I0.5000.35
166_D448_T0.5000.35
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  
4qiwB 1 0.9812 100 0.038 Contact Map
4aybB 1 0.9875 100 0.045 Contact Map
3h0gB 1 0.9708 100 0.061 Contact Map
1twfB 2 0.9396 100 0.064 Contact Map
4c2mB 1 0.9896 100 0.11 Contact Map
4yfkC 1 0.8938 100 0.203 Contact Map
2a6hC 1 0.8771 100 0.204 Contact Map
4kbmA 1 0.6979 100 0.435 Contact Map
3mlqA 1 0.3604 100 0.711 Contact Map
3ltiA 1 0.3083 99.9 0.81 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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