GREMLIN Database
RPOB - DNA-directed RNA polymerase subunit beta
UniProt: P37870 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 1193 (1150)
Sequences: 517 (197)
Seq/√Len: 5.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
762_G953_I10.7921.00
679_P737_V8.7971.00
38_Q42_D7.8291.00
12_R986_H7.0271.00
692_V742_L7.0061.00
562_D610_Y6.6261.00
678_H708_D6.3151.00
683_E693_R5.9160.99
780_R954_D5.4610.99
695_Y735_E5.3350.99
625_C753_L5.3190.99
694_R708_D5.1960.99
776_I956_M5.1400.98
655_A986_H4.9750.98
17_Y1003_T4.8460.98
677_K708_D4.5560.97
1012_D1029_R4.2840.95
1005_E1011_R4.2050.95
683_E707_L4.1450.94
582_D586_A4.0870.94
775_I1037_M3.9140.92
827_R907_Q3.9060.92
761_V1037_M3.8570.92
12_R655_A3.7470.90
1018_Y1029_R3.7430.90
653_P757_R3.5790.88
155_K178_D3.5660.88
775_I787_Y3.5490.88
146_F162_V3.4740.86
290_L310_L3.2830.83
1018_Y1025_P3.2820.83
11_H734_D3.2700.83
1146_S1150_E3.1420.80
290_L304_A3.1080.79
572_Y610_Y3.0540.78
777_M935_I3.0070.77
673_A748_M2.9640.76
424_L431_V2.9150.74
622_A1095_I2.8340.72
46_R68_D2.8320.72
778_S941_E2.8320.72
759_V954_D2.8020.71
532_S775_I2.7620.70
78_V111_V2.7210.69
379_A1043_M2.7180.69
759_V787_Y2.6890.68
676_C708_D2.6660.67
557_V581_L2.6570.67
15_R1006_E2.6430.67
549_R610_Y2.6290.66
974_L1031_S2.6260.66
981_R1034_I2.6200.66
186_R530_S2.5990.65
90_A118_I2.5860.65
254_L898_G2.5650.64
920_S938_I2.4940.62
935_I1037_M2.4560.61
478_A986_H2.4390.60
787_Y915_Q2.4130.59
549_R562_D2.3940.59
787_Y1037_M2.3530.57
127_I136_S2.3490.57
290_L308_Q2.3490.57
820_A1095_I2.3250.56
780_R941_E2.3080.56
654_E757_R2.3000.55
213_E218_R2.2830.55
304_A310_L2.2700.54
196_L385_I2.2690.54
714_K725_N2.2260.53
693_R707_L2.2040.52
777_M1048_L2.1920.52
304_A308_Q2.1860.51
71_L92_L2.1660.51
180_V389_F2.1620.50
951_T1036_Y2.1600.50
579_A587_F2.1570.50
654_E981_R2.1490.50
787_Y954_D2.1430.50
980_A987_I2.1430.50
560_R610_Y2.1380.50
530_S617_Q2.1370.50
545_T617_Q2.1100.49
691_W707_L2.1040.48
678_H694_R2.1020.48
41_L687_A2.0880.48
762_G1017_L2.0810.48
718_S909_V2.0810.48
978_M1015_T2.0760.47
497_E1146_S2.0670.47
948_P1015_T2.0650.47
1057_S1064_L2.0620.47
888_H914_V2.0320.46
668_K741_I2.0160.45
65_E99_I2.0090.45
29_L1085_A1.9840.44
679_P695_Y1.9760.44
1124_V1142_V1.9660.44
1012_D1018_Y1.9580.43
204_D227_E1.9530.43
257_S409_L1.9530.43
409_L761_V1.9480.43
759_V1036_Y1.9440.43
365_G368_Y1.9330.43
654_E939_L1.9290.42
162_V172_Y1.9220.42
532_S757_R1.9200.42
204_D221_L1.9200.42
71_L118_I1.9120.42
495_T1090_Y1.8940.41
851_V862_H1.8930.41
734_D891_K1.8820.41
30_I574_V1.8710.40
304_A608_V1.8650.40
532_S1037_M1.8650.40
750_L986_H1.8550.40
432_R948_P1.8470.40
622_A926_A1.8420.39
714_K834_A1.8400.39
887_I911_V1.8230.39
662_M787_Y1.8190.39
778_S1003_T1.8130.38
342_V347_I1.8060.38
497_E775_I1.8060.38
529_N622_A1.7990.38
813_I1114_V1.7920.38
506_V564_L1.7900.38
815_N977_G1.7860.38
519_T635_N1.7840.38
97_R108_D1.7800.37
294_L1161_E1.7800.37
760_M953_I1.7790.37
240_L444_T1.7770.37
83_E887_I1.7730.37
116_F458_I1.7710.37
760_M1034_I1.7680.37
363_V366_N1.7670.37
748_M883_G1.7600.37
211_I532_S1.7490.36
678_H738_K1.7350.36
926_A1095_I1.7340.36
514_M821_L1.7250.36
1016_V1025_P1.7240.36
54_P466_Q1.7180.35
183_R245_P1.7070.35
255_L262_P1.7060.35
530_S564_L1.7040.35
61_N641_A1.7040.35
195_L1103_V1.7000.35
594_A608_V1.6990.35
290_L294_L1.6990.35
486_L734_D1.6940.35
138_L853_E1.6920.35
124_T664_Y1.6910.35
1031_S1043_M1.6880.34
305_E308_Q1.6730.34
202_G232_A1.6720.34
17_Y122_T1.6710.34
1016_V1029_R1.6500.33
795_Y935_I1.6440.33
1015_T1018_Y1.6410.33
1038_I1048_L1.6330.33
333_P337_V1.6320.33
385_I896_E1.6310.33
374_K886_I1.6300.33
556_K1148_D1.6270.33
186_R268_A1.6230.32
562_D568_E1.6180.32
1121_E1156_D1.6080.32
333_P336_G1.6070.32
776_I1048_L1.6070.32
240_L1008_G1.5970.32
77_P81_S1.5900.31
263_K1109_T1.5880.31
350_F798_E1.5840.31
545_T953_I1.5800.31
780_R784_D1.5790.31
152_K1035_M1.5780.31
722_T1036_Y1.5760.31
585_G689_N1.5750.31
269_N539_R1.5750.31
747_S935_I1.5700.31
532_S761_V1.5660.31
54_P617_Q1.5650.31
254_L429_R1.5540.30
71_L497_E1.5540.30
361_I365_G1.5520.30
172_Y384_S1.5390.30
201_F382_I1.5360.30
92_L106_V1.5300.30
684_R689_N1.5220.29
689_N709_K1.5170.29
977_G1032_V1.5110.29
201_F210_L1.5110.29
146_F172_Y1.5090.29
893_F1046_D1.5090.29
867_E987_I1.4950.29
187_T617_Q1.4890.28
18_A282_K1.4890.28
610_Y971_V1.4870.28
878_R953_I1.4850.28
731_S734_D1.4730.28
1121_E1147_G1.4720.28
658_V708_D1.4690.28
915_Q1046_D1.4690.28
124_T485_R1.4680.28
170_L182_V1.4670.28
686_E689_N1.4640.28
598_G618_V1.4630.28
50_Q206_E1.4610.28
303_L317_K1.4600.28
48_M170_L1.4530.27
568_E734_D1.4510.27
894_N897_D1.4480.27
290_L303_L1.4460.27
32_I545_T1.4450.27
616_K635_N1.4430.27
81_S855_T1.4410.27
598_G1037_M1.4390.27
555_G586_A1.4390.27
28_N35_S1.4370.27
545_T762_G1.4340.27
192_V856_A1.4320.27
949_D1036_Y1.4320.27
618_V641_A1.4270.27
759_V1037_M1.4270.27
177_K1038_I1.4260.27
1001_W1011_R1.4250.27
761_V765_T1.4240.27
245_P948_P1.4230.27
304_A307_G1.4230.27
132_R448_L1.4110.26
838_D1038_I1.4070.26
759_V949_D1.4060.26
65_E97_R1.4020.26
664_Y741_I1.4010.26
247_T1114_V1.3990.26
749_E754_A1.3960.26
674_V998_E1.3950.26
253_S257_S1.3940.26
759_V780_R1.3910.26
39_W44_G1.3900.26
126_I255_L1.3890.26
485_R1091_T1.3870.26
395_V890_V1.3850.26
878_R960_L1.3750.25
87_T409_L1.3750.25
594_A603_V1.3740.25
436_S495_T1.3710.25
708_D738_K1.3710.25
713_L716_V1.3690.25
995_A1000_V1.3640.25
469_Q507_H1.3640.25
742_L997_E1.3620.25
32_I795_Y1.3600.25
463_G910_R1.3580.25
775_I1143_K1.3580.25
497_E539_R1.3550.25
158_F893_F1.3550.25
509_S827_R1.3550.25
192_V385_I1.3540.25
915_Q968_I1.3510.25
777_M1129_K1.3480.25
202_G228_N1.3470.25
658_V778_S1.3440.25
474_T949_D1.3440.25
509_S681_I1.3400.24
184_I625_C1.3390.24
556_K584_E1.3370.24
71_L816_V1.3360.24
1143_K1151_E1.3350.24
376_I708_D1.3310.24
81_S1043_M1.3310.24
239_R908_L1.3280.24
112_F1147_G1.3280.24
935_I1162_D1.3270.24
574_V926_A1.3260.24
345_Q978_M1.3240.24
570_D839_G1.3220.24
292_E754_A1.3180.24
400_D485_R1.3170.24
144_V275_I1.3120.24
474_T759_V1.3070.24
658_V1003_T1.3050.24
196_L211_I1.3040.23
523_P1091_T1.3020.23
509_S907_Q1.3000.23
616_K622_A1.2890.23
684_R1031_S1.2890.23
190_L236_I1.2890.23
238_E258_R1.2890.23
659_G754_A1.2870.23
514_M816_V1.2830.23
1029_R1059_V1.2810.23
979_A1007_A1.2790.23
85_D168_A1.2790.23
201_F778_S1.2790.23
631_N953_I1.2780.23
79_E711_S1.2780.23
954_D1007_A1.2740.23
662_M775_I1.2730.23
549_R560_R1.2730.23
172_Y938_I1.2720.23
708_D1008_G1.2690.23
514_M635_N1.2680.23
580_R589_D1.2670.23
544_E852_T1.2660.23
776_I862_H1.2650.23
454_V623_T1.2640.23
622_A820_A1.2630.22
692_V894_N1.2580.22
938_I956_M1.2560.22
349_I367_A1.2540.22
679_P735_E1.2530.22
60_G1002_E1.2510.22
568_E657_F1.2490.22
533_S597_R1.2470.22
34_T1009_M1.2460.22
987_I1153_E1.2450.22
711_S938_I1.2430.22
497_E757_R1.2410.22
590_D621_A1.2410.22
186_R754_A1.2390.22
611_M799_A1.2380.22
68_D819_D1.2370.22
67_I95_K1.2340.22
1000_V1003_T1.2340.22
488_A1113_I1.2330.22
953_I1017_L1.2330.22
81_S84_R1.2310.22
914_V956_M1.2310.22
367_A370_E1.2290.22
17_Y290_L1.2280.22
466_Q530_S1.2260.22
65_E236_I1.2240.22
320_P761_V1.2240.22
1025_P1029_R1.2230.22
763_F1035_M1.2230.22
681_I735_E1.2180.21
512_G545_T1.2180.21
409_L509_S1.2180.21
409_L529_N1.2150.21
241_R608_V1.2120.21
149_K437_I1.2120.21
26_L665_V1.2110.21
172_Y176_A1.2110.21
47_E812_D1.2110.21
196_L617_Q1.2100.21
385_I795_Y1.2100.21
782_V955_I1.2100.21
624_A673_A1.2100.21
556_K586_A1.2090.21
338_V348_K1.2090.21
180_V1142_V1.2080.21
775_I1034_I1.2080.21
474_T761_V1.2060.21
593_V935_I1.2060.21
635_N926_A1.2040.21
263_K736_V1.2030.21
561_I787_Y1.2030.21
326_I478_A1.2000.21
448_L1059_V1.1970.21
275_I987_I1.1970.21
436_S447_Q1.1940.21
254_L400_D1.1930.21
941_E954_D1.1920.21
254_L424_L1.1890.21
1111_E1115_K1.1820.21
862_H883_G1.1820.21
816_V820_A1.1820.21
587_F611_M1.1790.20
364_I705_G1.1770.20
926_A1046_D1.1770.20
407_R1068_A1.1740.20
359_Q778_S1.1740.20
573_V594_A1.1740.20
215_E539_R1.1720.20
439_D561_I1.1700.20
12_R750_L1.1650.20
126_I572_Y1.1640.20
204_D228_N1.1640.20
34_T598_G1.1640.20
851_V883_G1.1630.20
908_L941_E1.1620.20
121_D775_I1.1600.20
759_V951_T1.1600.20
617_Q668_K1.1590.20
17_Y1121_E1.1580.20
1153_E1156_D1.1580.20
90_A456_A1.1530.20
390_N715_F1.1520.20
1048_L1129_K1.1510.20
746_P815_N1.1500.20
610_Y692_V1.1490.20
449_I822_R1.1490.20
478_A529_N1.1490.20
534_Y658_V1.1470.20
456_A523_P1.1460.20
532_S596_F1.1460.20
949_D1135_L1.1440.20
54_P530_S1.1430.20
777_M1038_I1.1430.20
62_L105_E1.1430.20
87_T1103_V1.1420.20
305_E455_I1.1410.20
570_D597_R1.1410.20
319_L938_I1.1410.20
578_N616_K1.1380.20
337_V432_R1.1340.19
466_Q617_Q1.1310.19
625_C673_A1.1310.19
686_E887_I1.1300.19
177_K883_G1.1290.19
392_L762_G1.1280.19
202_G229_S1.1270.19
201_F532_S1.1270.19
239_R736_V1.1250.19
304_A761_V1.1240.19
978_M1009_M1.1230.19
652_Q1103_V1.1220.19
429_R796_E1.1200.19
555_G1036_Y1.1190.19
351_A360_V1.1180.19
619_V991_V1.1180.19
538_N801_D1.1180.19
66_F85_D1.1170.19
1000_V1004_L1.1170.19
659_G664_Y1.1160.19
21_S742_L1.1160.19
87_T891_K1.1160.19
304_A1037_M1.1150.19
586_A611_M1.1150.19
429_R812_D1.1140.19
793_E1093_Q1.1140.19
759_V778_S1.1130.19
536_K956_M1.1120.19
804_L1059_V1.1100.19
26_L529_N1.1060.19
30_I911_V1.1040.19
285_L1139_G1.1030.19
459_K747_S1.1010.19
778_S1041_A1.1000.19
146_F938_I1.0980.19
723_C820_A1.0980.19
625_C1004_L1.0980.19
240_L435_M1.0970.19
761_V783_K1.0940.19
651_M812_D1.0930.19
812_D1132_I1.0930.19
217_L655_A1.0910.19
971_V978_M1.0900.19
741_I801_D1.0870.18
45_L485_R1.0860.18
153_N592_I1.0840.18
424_L778_S1.0830.18
382_I783_K1.0820.18
321_Y790_I1.0820.18
19_R57_D1.0790.18
289_R309_I1.0790.18
532_S790_I1.0780.18
555_G887_I1.0740.18
685_V890_V1.0730.18
62_L103_T1.0730.18
459_K812_D1.0720.18
448_L804_L1.0720.18
52_I310_L1.0670.18
41_L616_K1.0650.18
186_R466_Q1.0640.18
853_E1143_K1.0640.18
18_A1090_Y1.0630.18
940_P980_A1.0620.18
180_V617_Q1.0610.18
186_R988_A1.0600.18
18_A42_D1.0600.18
946_Y1018_Y1.0600.18
100_N103_T1.0590.18
254_L433_E1.0580.18
757_R939_L1.0570.18
172_Y753_L1.0570.18
192_V358_E1.0570.18
938_I1137_S1.0570.18
441_N1089_A1.0560.18
53_S910_R1.0550.18
345_Q348_K1.0550.18
995_A1070_F1.0530.18
54_P186_R1.0530.18
1004_L1013_A1.0520.18
470_F528_I1.0510.18
537_V709_K1.0510.18
179_V729_I1.0500.18
590_D747_S1.0490.18
86_V817_G1.0480.18
759_V775_I1.0460.18
308_Q311_D1.0460.18
1010_S1015_T1.0450.18
621_A739_G1.0440.18
241_R244_E1.0430.18
578_N631_N1.0420.18
182_V1002_E1.0410.18
577_A580_R1.0390.17
17_Y250_N1.0380.17
257_S529_N1.0380.17
625_C748_M1.0370.17
121_D818_E1.0350.17
75_K903_P1.0350.17
205_Q827_R1.0340.17
579_A589_D1.0330.17
617_Q753_L1.0320.17
134_I734_D1.0300.17
616_K742_L1.0290.17
722_T934_V1.0280.17
87_T621_A1.0280.17
196_L199_L1.0250.17
742_L746_P1.0250.17
389_F1002_E1.0240.17
443_I911_V1.0240.17
11_H17_Y1.0230.17
400_D898_G1.0220.17
197_R268_A1.0220.17
474_T721_G1.0220.17
409_L954_D1.0210.17
244_E1012_D1.0200.17
540_F742_L1.0180.17
849_K942_E1.0170.17
1104_V1132_I1.0160.17
587_F692_V1.0150.17
113_M1098_V1.0140.17
192_V812_D1.0130.17
195_L674_V1.0120.17
59_T253_S1.0100.17
162_V817_G1.0100.17
795_Y1048_L1.0090.17
135_V550_V1.0080.17
92_L1108_K1.0060.17
720_Q960_L1.0050.17
247_T497_E1.0050.17
621_A662_M1.0050.17
861_L864_I1.0050.17
489_L499_A1.0040.17
347_I953_I1.0030.17
534_Y911_V1.0030.17
56_E63_S1.0020.17
809_I999_D1.0010.17
508_Y574_V1.0010.17
293_T305_E1.0000.17
82_K239_R1.0000.17
715_F830_I0.9990.17
469_Q482_H0.9970.17
196_L568_E0.9950.17
78_V82_K0.9950.17
371_E953_I0.9940.17
1006_E1034_I0.9940.17
474_T1037_M0.9910.17
49_F429_R0.9900.17
162_V734_D0.9900.17
12_R659_G0.9890.17
576_Q1027_D0.9890.17
725_N834_A0.9880.16
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57_D873_R0.5070.09
71_L784_D0.5060.09
173_E741_I0.5060.09
509_S1143_K0.5060.09
767_D910_R0.5060.09
515_C722_T0.5060.09
1123_G1131_L0.5060.09
549_R564_L0.5050.09
21_S209_D0.5050.09
144_V951_T0.5050.09
101_K255_L0.5040.09
152_K765_T0.5040.09
143_S851_V0.5040.09
250_N759_V0.5040.09
354_D741_I0.5030.09
584_E1149_E0.5030.09
118_I560_R0.5030.09
363_V367_A0.5030.09
205_Q1053_T0.5030.09
162_V713_L0.5030.09
338_V352_P0.5020.09
552_P859_R0.5020.09
266_D498_R0.5020.09
424_L1007_A0.5020.09
529_N555_G0.5020.09
30_I441_N0.5010.09
389_F535_A0.5010.09
239_R255_L0.5010.09
956_M1037_M0.5010.09
228_N497_E0.5010.09
555_G1037_M0.5010.09
395_V1112_A0.5000.09
138_L433_E0.5000.09
585_G801_D0.5000.09
734_D993_D0.5000.09
753_L953_I0.5000.09
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  
4yfkC 1 0.8826 100 0.245 Contact Map
2a6hC 1 0.8868 100 0.29 Contact Map
4qiwB 1 0.7435 100 0.456 Contact Map
4aybB 1 0.7678 100 0.459 Contact Map
3h0gB 1 0.7787 100 0.46 Contact Map
1twfB 2 0.7477 100 0.467 Contact Map
4c2mB 1 0.7988 100 0.564 Contact Map
4kbmA 1 0.2984 100 0.811 Contact Map
3mlqA 1 0.1459 100 0.898 Contact Map
3ltiA 1 0.1358 100 0.907 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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