GREMLIN Database
RPOB2 - DNA-directed RNA polymerase subunit B''
UniProt: P0CX04 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 523 (448)
Sequences: 2421 (1197)
Seq/√Len: 56.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
230_F329_A6.5151.00
21_E25_R6.3941.00
315_E331_A5.9151.00
36_Q62_L5.5111.00
36_Q64_D4.9171.00
68_V97_P4.8631.00
270_T273_E4.5391.00
36_Q40_T4.4161.00
64_D101_E3.3681.00
217_L333_F3.3401.00
61_E103_S3.1761.00
46_E59_W3.1411.00
439_L463_I3.0461.00
86_E90_R2.9731.00
62_L372_A2.9431.00
268_V274_A2.9141.00
239_L248_R2.8891.00
166_R421_S2.8641.00
306_H488_Q2.8221.00
243_E247_H2.8141.00
28_N32_E2.7711.00
141_S144_E2.7511.00
26_S357_G2.6851.00
434_S479_N2.6181.00
194_A198_S2.5031.00
29_A33_H2.4211.00
334_E340_R2.3681.00
59_W105_V2.3451.00
498_Q509_P2.2731.00
198_S201_R2.2651.00
277_D280_Q2.2431.00
196_T201_R2.1871.00
109_E139_G2.1321.00
480_F492_D2.1281.00
235_R242_D2.1241.00
66_R99_F2.0931.00
334_E339_R2.0661.00
262_N266_A2.0501.00
271_Q275_I2.0411.00
248_R326_C2.0091.00
422_Q456_H2.0011.00
96_A153_A1.9971.00
106_R109_E1.9831.00
140_F144_E1.9701.00
63_G103_S1.9691.00
271_Q294_R1.9681.00
432_V436_L1.9421.00
487_S493_E1.9261.00
37_D40_T1.9191.00
194_A201_R1.9181.00
263_L266_A1.9001.00
290_Y293_K1.8961.00
29_A34_G1.8430.99
24_F28_N1.8280.99
43_E102_M1.8100.99
434_S467_E1.7870.99
234_V326_C1.7800.99
289_N292_L1.7690.99
335_L342_A1.7440.99
68_V96_A1.7360.99
500_L503_M1.7180.99
209_V328_M1.7080.99
467_E479_N1.6860.99
196_T209_V1.6670.99
291_Q295_A1.6560.99
351_K413_W1.6440.99
233_L325_L1.6440.99
217_L230_F1.6320.99
290_Y294_R1.6260.99
38_V41_E1.6180.99
259_M262_N1.6150.99
395_V399_V1.6050.99
441_S459_Q1.6010.98
234_V239_L1.5900.98
196_T200_R1.5900.98
240_E271_Q1.5860.98
68_V99_F1.5820.98
206_L209_V1.5650.98
257_K261_E1.5610.98
35_M65_V1.5560.98
394_V463_I1.5550.98
500_L505_V1.5470.98
239_L322_A1.5080.98
467_E470_E1.5050.98
172_E407_P1.4970.98
103_S143_E1.4900.98
73_R87_A1.4890.98
288_K292_L1.4690.97
38_V42_K1.4650.97
239_L245_I1.4580.97
333_F337_L1.4570.97
192_Q198_S1.4530.97
234_V329_A1.4470.97
35_M364_F1.4270.97
359_L433_L1.4130.97
499_E504_G1.4130.97
189_D194_A1.3920.96
26_S165_E1.3770.96
228_I381_R1.3710.96
230_F325_L1.3710.96
160_I320_N1.3670.96
258_F261_E1.3590.96
438_R467_E1.3520.96
21_E485_E1.3490.96
207_V211_R1.3450.96
331_A340_R1.3410.95
32_E161_I1.3390.95
423_L432_V1.3350.95
436_L467_E1.3330.95
170_T353_L1.3320.95
416_G479_N1.3250.95
406_H413_W1.3240.95
166_R416_G1.3090.95
63_G101_E1.3040.95
261_E264_E1.3020.95
412_N423_L1.3010.95
70_P73_R1.2860.94
424_V436_L1.2860.94
35_M64_D1.2780.94
453_R475_G1.2770.94
172_E478_K1.2760.94
37_D361_K1.2740.94
422_Q438_R1.2720.94
453_R464_C1.2670.94
257_K263_L1.2640.94
194_A199_Q1.2530.93
232_T268_V1.2520.93
245_I329_A1.2520.93
344_D456_H1.2420.93
178_K328_M1.2420.93
259_M329_A1.2400.93
207_V325_L1.2390.93
34_G361_K1.2330.93
288_K291_Q1.2290.93
267_D364_F1.2280.93
422_Q435_H1.2220.93
471_G475_G1.2210.93
391_V395_V1.2200.93
462_R473_N1.2180.92
182_E190_E1.2170.92
152_P421_S1.2120.92
246_V260_L1.2060.92
140_F148_I1.2050.92
6_K13_Y1.2040.92
333_F336_A1.2040.92
235_R267_D1.2030.92
276_E280_Q1.2010.92
317_T321_K1.1990.92
345_K351_K1.1920.92
215_G329_A1.1890.92
464_C468_T1.1740.91
326_C330_E1.1600.90
219_V230_F1.1600.90
240_E244_E1.1490.90
58_V104_I1.1460.90
290_Y295_A1.1450.90
351_K449_H1.1420.90
300_D318_R1.1420.90
335_L340_R1.1420.90
404_L408_I1.1370.90
259_M333_F1.1330.89
158_Y410_T1.1330.89
195_K443_L1.1330.89
242_D268_V1.1300.89
500_L504_G1.1290.89
291_Q294_R1.1270.89
455_L474_C1.1260.89
312_V317_T1.1250.89
184_D187_Y1.1240.89
156_G181_A1.1230.89
30_F407_P1.1170.89
255_I258_F1.1160.89
194_A200_R1.1160.89
225_S282_V1.1150.89
461_G494_R1.1140.89
165_E235_R1.1110.88
196_T328_M1.1070.88
445_R473_N1.1030.88
443_L452_A1.0950.88
27_Y298_V1.0930.88
106_R144_E1.0920.88
209_V332_C1.0910.88
88_R156_G1.0880.87
245_I249_V1.0860.87
244_E247_H1.0850.87
25_R29_A1.0810.87
252_D255_I1.0780.87
506_E509_P1.0690.86
65_V98_V1.0650.86
140_F143_E1.0650.86
166_R206_L1.0610.86
259_M263_L1.0610.86
18_R24_F1.0530.86
505_V509_P1.0460.85
46_E50_G1.0430.85
450_F454_D1.0390.85
248_R330_E1.0370.85
156_G408_I1.0310.84
406_H410_T1.0300.84
464_C471_G1.0270.84
460_W474_C1.0260.84
498_Q507_G1.0250.84
438_R470_E1.0240.84
351_K438_R1.0210.84
208_L474_C1.0210.84
258_F262_N1.0210.84
20_A301_R1.0180.84
31_L40_T1.0180.84
453_R471_G1.0120.83
501_S504_G1.0090.83
67_A98_V1.0090.83
416_G467_E1.0080.83
228_I233_L1.0070.83
252_D258_F1.0060.83
145_L150_E0.9990.83
435_H473_N0.9940.82
25_R28_N0.9920.82
377_Y381_R0.9920.82
353_L486_L0.9910.82
425_D432_V0.9880.82
500_L507_G0.9810.81
45_I48_D0.9770.81
391_V394_V0.9770.81
445_R467_E0.9760.81
505_V508_I0.9720.81
93_T161_I0.9720.81
290_Y463_I0.9700.81
470_E477_V0.9630.80
196_T207_V0.9580.80
375_V394_V0.9580.80
428_D466_S0.9580.80
406_H409_A0.9580.80
454_D462_R0.9560.80
500_L508_I0.9530.79
30_F360_M0.9500.79
392_N396_R0.9500.79
503_M506_E0.9500.79
289_N295_A0.9480.79
22_H480_F0.9450.79
249_V259_M0.9440.79
465_P468_T0.9430.79
41_E361_K0.9420.79
370_K374_D0.9360.78
29_A361_K0.9350.78
98_V266_A0.9350.78
169_M443_L0.9340.78
210_E220_S0.9320.78
197_F201_R0.9320.78
499_E502_S0.9290.78
296_N303_L0.9250.77
165_E357_G0.9220.77
91_N363_L0.9160.77
481_A494_R0.9150.77
14_F412_N0.9100.76
274_A438_R0.9100.76
103_S145_L0.9080.76
312_V316_E0.9050.76
194_A332_C0.9030.76
207_V212_N0.9030.76
465_P469_P0.9020.76
41_E365_R0.9020.76
422_Q467_E0.9010.75
18_R21_E0.9010.75
485_E493_E0.9000.75
456_H470_E0.8970.75
182_E185_S0.8950.75
98_V364_F0.8940.75
156_G508_I0.8930.75
297_Y301_R0.8910.75
167_V422_Q0.8900.75
38_V361_K0.8900.75
283_A286_Q0.8830.74
20_A433_L0.8800.74
32_E37_D0.8790.74
456_H459_Q0.8790.74
248_R323_Y0.8780.74
232_T328_M0.8750.73
42_K45_I0.8750.73
497_K505_V0.8750.73
228_I278_L0.8730.73
167_V438_R0.8720.73
161_I170_T0.8710.73
66_R145_L0.8700.73
379_L486_L0.8690.73
276_E290_Y0.8670.73
168_L191_I0.8580.72
88_R160_I0.8580.72
32_E393_T0.8570.72
373_R409_A0.8520.71
438_R459_Q0.8510.71
33_H37_D0.8490.71
168_L293_K0.8480.71
453_R468_T0.8450.71
29_A37_D0.8440.71
330_E339_R0.8430.70
156_G314_E0.8390.70
461_G475_G0.8390.70
407_P458_T0.8380.70
247_H251_E0.8380.70
398_D433_L0.8330.70
269_Q273_E0.8320.69
255_I337_L0.8300.69
40_T46_E0.8280.69
503_M507_G0.8260.69
88_R165_E0.8230.69
498_Q501_S0.8210.68
289_N294_R0.8210.68
20_A418_S0.8160.68
139_G282_V0.8160.68
372_A376_K0.8140.68
325_L329_A0.8130.68
422_Q470_E0.8110.68
45_I162_N0.8080.67
187_Y190_E0.8080.67
209_V213_R0.8070.67
500_L506_E0.8070.67
95_S150_E0.8070.67
42_K49_I0.8070.67
238_G245_I0.8040.67
448_P452_A0.8020.67
195_K225_S0.8010.67
156_G242_D0.8000.66
168_L421_S0.7990.66
272_E294_R0.7980.66
221_F278_L0.7970.66
374_D378_Q0.7950.66
99_F486_L0.7950.66
368_L433_L0.7940.66
44_R373_R0.7940.66
423_L426_R0.7930.66
186_K305_P0.7910.66
441_S467_E0.7880.65
219_V295_A0.7880.65
395_V398_D0.7870.65
33_H36_Q0.7870.65
167_V353_L0.7840.65
443_L450_F0.7840.65
218_E458_T0.7830.65
160_I253_P0.7820.65
480_F486_L0.7820.65
144_E147_E0.7810.65
57_P364_F0.7780.64
11_E67_A0.7760.64
442_P456_H0.7730.64
458_T467_E0.7730.64
67_A96_A0.7720.64
98_V223_S0.7700.63
312_V321_K0.7690.63
272_E290_Y0.7690.63
106_R390_T0.7670.63
468_T475_G0.7650.63
174_L309_E0.7640.63
235_R268_V0.7640.63
61_E105_V0.7630.63
108_G272_E0.7630.63
151_D156_G0.7620.63
427_T463_I0.7610.63
452_A477_V0.7590.62
100_M368_L0.7590.62
193_V245_I0.7580.62
299_I306_H0.7550.62
434_S451_E0.7540.62
413_W417_R0.7540.62
105_V108_G0.7510.62
163_G471_G0.7500.61
33_H40_T0.7470.61
195_K199_Q0.7470.61
87_A90_R0.7470.61
59_W107_G0.7460.61
304_L359_L0.7460.61
10_S20_A0.7460.61
143_E147_E0.7430.61
426_R432_V0.7420.61
208_L459_Q0.7410.60
378_Q396_R0.7400.60
99_F143_E0.7370.60
416_G435_H0.7370.60
234_V325_L0.7370.60
43_E47_T0.7370.60
89_L214_E0.7350.60
191_I211_R0.7340.60
353_L463_I0.7300.59
70_P74_E0.7290.59
231_V263_L0.7280.59
257_K260_L0.7280.59
25_R507_G0.7270.59
6_K11_E0.7250.59
358_D414_V0.7240.59
106_R139_G0.7230.59
443_L451_E0.7210.58
451_E454_D0.7180.58
165_E469_P0.7180.58
350_N415_G0.7160.58
186_K247_H0.7150.58
87_A93_T0.7120.57
288_K293_K0.7110.57
63_G395_V0.7110.57
259_M266_A0.7100.57
190_E194_A0.7070.57
375_V397_S0.7070.57
11_E14_F0.7070.57
18_R22_H0.7050.57
58_V107_G0.7020.56
193_V201_R0.7010.56
218_E227_S0.7000.56
187_Y196_T0.6990.56
444_S473_N0.6990.56
462_R466_S0.6980.56
26_S355_V0.6970.56
201_R207_V0.6950.56
10_S13_Y0.6940.55
43_E61_E0.6910.55
425_D428_D0.6910.55
309_E490_V0.6900.55
7_R332_C0.6870.55
443_L448_P0.6840.54
450_F473_N0.6840.54
363_L407_P0.6810.54
102_M233_L0.6800.54
57_P66_R0.6800.54
254_E257_K0.6800.54
424_V431_G0.6790.54
374_D377_Y0.6770.54
156_G312_V0.6730.53
342_A375_V0.6720.53
8_E12_S0.6720.53
90_R357_G0.6710.53
26_S435_H0.6710.53
428_D437_R0.6710.53
91_N98_V0.6700.53
374_D394_V0.6690.53
501_S507_G0.6660.52
371_L379_L0.6660.52
39_V97_P0.6650.52
424_V452_A0.6650.52
212_N218_E0.6640.52
19_L433_L0.6630.52
248_R353_L0.6630.52
370_K399_V0.6610.52
207_V210_E0.6600.52
259_M330_E0.6590.52
423_L436_L0.6590.52
331_A335_L0.6580.52
283_A291_Q0.6560.51
219_V233_L0.6550.51
464_C475_G0.6540.51
262_N275_I0.6540.51
449_H479_N0.6510.51
62_L368_L0.6500.51
470_E479_N0.6500.51
256_V260_L0.6490.51
314_E317_T0.6480.51
426_R446_S0.6480.51
6_K9_L0.6460.50
424_V482_Q0.6440.50
282_V285_G0.6430.50
169_M437_R0.6430.50
267_D273_E0.6430.50
208_L211_R0.6420.50
230_F353_L0.6420.50
212_N289_N0.6410.50
29_A358_D0.6400.50
168_L356_S0.6390.50
308_H343_D0.6390.50
435_H479_N0.6360.49
459_Q467_E0.6360.49
162_N405_E0.6350.49
455_L465_P0.6310.49
166_R192_Q0.6310.49
184_D190_E0.6300.49
503_M509_P0.6280.48
43_E377_Y0.6270.48
288_K295_A0.6260.48
375_V391_V0.6250.48
345_K447_Q0.6250.48
67_A502_S0.6250.48
447_Q454_D0.6240.48
10_S457_A0.6240.48
188_G353_L0.6240.48
343_D350_N0.6230.48
350_N430_M0.6220.48
27_Y62_L0.6210.48
252_D337_L0.6200.47
501_S505_V0.6180.47
185_S338_G0.6180.47
416_G441_S0.6160.47
227_S370_K0.6160.47
247_H498_Q0.6160.47
348_Y432_V0.6160.47
152_P422_Q0.6160.47
425_D431_G0.6150.47
502_S507_G0.6140.47
284_S287_G0.6140.47
189_D192_Q0.6130.47
453_R470_E0.6090.46
250_S439_L0.6080.46
408_I411_G0.6080.46
88_R281_R0.6060.46
179_I194_A0.6050.46
46_E105_V0.6040.46
156_G419_G0.6030.46
13_Y497_K0.6000.45
451_E467_E0.6000.45
422_Q432_V0.5990.45
260_L509_P0.5980.45
406_H412_N0.5950.45
201_R206_L0.5940.45
16_K482_Q0.5930.45
196_T199_Q0.5930.45
262_N350_N0.5930.45
364_F411_G0.5920.44
109_E140_F0.5920.44
242_D270_T0.5910.44
48_D376_K0.5910.44
246_V278_L0.5910.44
97_P149_G0.5910.44
464_C469_P0.5890.44
275_I296_N0.5890.44
461_G468_T0.5880.44
255_I260_L0.5880.44
152_P470_E0.5880.44
39_V377_Y0.5870.44
41_E46_E0.5870.44
25_R488_Q0.5870.44
466_S473_N0.5860.44
290_Y376_K0.5850.44
28_N38_V0.5850.44
232_T274_A0.5830.43
9_L158_Y0.5830.43
304_L439_L0.5830.43
7_R424_V0.5830.43
237_L312_V0.5830.43
235_R312_V0.5820.43
420_V426_R0.5810.43
332_C336_A0.5800.43
151_D154_D0.5800.43
507_G510_G0.5800.43
348_Y459_Q0.5800.43
158_Y165_E0.5790.43
371_L405_E0.5790.43
139_G336_A0.5780.43
447_Q472_P0.5770.43
233_L248_R0.5770.43
508_I511_I0.5740.42
437_R456_H0.5730.42
448_P454_D0.5720.42
287_G292_L0.5710.42
23_H169_M0.5710.42
210_E481_A0.5700.42
188_G191_I0.5690.42
172_E451_E0.5680.42
268_V273_E0.5680.42
206_L418_S0.5670.42
151_D411_G0.5670.42
68_V269_Q0.5660.42
285_G301_R0.5640.41
171_S440_R0.5640.41
499_E503_M0.5630.41
351_K367_A0.5620.41
235_R265_E0.5620.41
269_Q391_V0.5620.41
146_I375_V0.5620.41
504_G510_G0.5610.41
425_D436_L0.5610.41
453_R461_G0.5600.41
174_L442_P0.5600.41
505_V510_G0.5590.41
438_R445_R0.5590.41
158_Y356_S0.5590.41
335_L338_G0.5590.41
103_S141_S0.5580.41
34_G166_R0.5580.41
456_H467_E0.5580.41
338_G341_E0.5570.41
315_E339_R0.5560.41
256_V263_L0.5530.40
185_S265_E0.5530.40
185_S379_L0.5530.40
14_F168_L0.5530.40
186_K317_T0.5520.40
195_K330_E0.5520.40
309_E324_Y0.5520.40
16_K511_I0.5510.40
88_R433_L0.5510.40
187_Y191_I0.5510.40
229_S366_T0.5510.40
443_L447_Q0.5510.40
15_S33_H0.5490.40
410_T413_W0.5480.40
372_A412_N0.5470.40
325_L512_S0.5460.40
165_E349_A0.5460.40
173_D195_K0.5460.40
354_K425_D0.5450.39
173_D458_T0.5440.39
423_L477_V0.5430.39
490_V499_E0.5430.39
99_F339_R0.5420.39
149_G356_S0.5420.39
94_Y98_V0.5420.39
39_V44_R0.5410.39
491_D494_R0.5410.39
154_D413_W0.5410.39
38_V217_L0.5400.39
415_G429_F0.5400.39
232_T335_L0.5380.39
398_D458_T0.5380.39
24_F66_R0.5370.39
446_S449_H0.5370.39
227_S429_F0.5360.39
231_V262_N0.5360.39
192_Q342_A0.5330.38
473_N477_V0.5330.38
351_K447_Q0.5330.38
427_T446_S0.5330.38
407_P410_T0.5320.38
377_Y380_E0.5310.38
216_L258_F0.5300.38
195_K435_H0.5300.38
445_R450_F0.5290.38
316_E332_C0.5290.38
105_V144_E0.5270.38
104_I302_Y0.5270.38
458_T470_E0.5270.38
312_V318_R0.5270.38
43_E100_M0.5260.37
171_S414_V0.5250.37
270_T463_I0.5250.37
251_E257_K0.5250.37
243_E290_Y0.5250.37
49_I57_P0.5250.37
208_L235_R0.5240.37
195_K478_K0.5230.37
60_V350_N0.5230.37
150_E478_K0.5230.37
152_P174_L0.5210.37
485_E488_Q0.5210.37
228_I325_L0.5180.37
139_G264_E0.5180.37
296_N302_Y0.5180.37
275_I295_A0.5170.37
229_S242_D0.5160.36
190_E196_T0.5150.36
229_S278_L0.5140.36
287_G293_K0.5130.36
169_M424_V0.5130.36
186_K220_S0.5130.36
172_E355_V0.5120.36
58_V394_V0.5110.36
50_G390_T0.5100.36
27_Y61_E0.5090.36
437_R454_D0.5090.36
18_R359_L0.5080.36
192_Q201_R0.5070.36
237_L322_A0.5060.35
312_V328_M0.5050.35
468_T471_G0.5050.35
40_T270_T0.5040.35
236_A284_S0.5040.35
232_T316_E0.5040.35
296_N308_H0.5040.35
291_Q304_L0.5040.35
23_H443_L0.5030.35
71_R74_E0.5020.35
440_R477_V0.5020.35
329_A506_E0.5020.35
142_D371_L0.5020.35
413_W419_G0.5010.35
484_M507_G0.5000.35
139_G245_I0.5000.35
305_P431_G0.5000.35
35_M228_I0.5000.35
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 0.9579 100 0.099 Contact Map
4aybB 1 0.9656 100 0.107 Contact Map
1twfB 2 0.9082 100 0.109 Contact Map
3h0gB 1 0.9426 100 0.111 Contact Map
4c2mB 1 0.9751 100 0.145 Contact Map
2a6hC 1 0.8853 100 0.229 Contact Map
4yfkC 1 0.8967 100 0.24 Contact Map
4kbmA 1 0.6539 100 0.489 Contact Map
3mlqA 1 0.3384 100 0.746 Contact Map
3ltiA 1 0.2945 99.9 0.832 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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