GREMLIN Database
RPOC - DNA-directed RNA polymerase subunit beta'
UniProt: P37871 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 1199 (1119)
Sequences: 2624 (1235)
Seq/√Len: 36.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
21_R96_E8.3261.00
672_I708_A6.6771.00
508_G512_E6.3511.00
683_V704_I5.6031.00
176_H229_D5.5141.00
707_A711_V5.3811.00
357_L457_V4.7961.00
675_E679_K4.7881.00
24_S94_H4.6391.00
165_K168_A4.5501.00
354_Q407_E4.4201.00
167_Q177_K4.3921.00
853_K860_V4.2091.00
146_K181_D4.1991.00
373_E377_K4.1791.00
367_K463_A4.1641.00
183_D186_K4.0481.00
1086_T1106_V4.0451.00
869_D872_K4.0321.00
668_D715_K3.8901.00
411_L423_I3.8851.00
354_Q429_T3.8391.00
128_V135_V3.7231.00
848_A862_V3.6661.00
675_E711_V3.5081.00
531_V562_V3.4951.00
1102_A1105_K3.4791.00
958_E962_A3.4681.00
538_A559_I3.4531.00
541_A550_T3.4431.00
815_E894_T3.4011.00
989_Q993_V3.3361.00
102_S227_I3.3201.00
1103_N1114_A3.3151.00
671_E675_E3.3031.00
373_E376_E3.0941.00
709_K742_T2.9931.00
509_A532_H2.9821.00
670_Q674_E2.9461.00
120_M135_V2.9361.00
874_L878_E2.9001.00
676_A704_I2.8851.00
513_G535_T2.8751.00
863_N866_E2.8641.00
825_L883_E2.8281.00
187_E213_L2.8121.00
854_H859_E2.7591.00
1099_F1116_G2.7421.00
955_R958_E2.7291.00
850_K885_W2.7191.00
170_M175_I2.7171.00
679_K682_N2.7131.00
508_G513_G2.7051.00
532_H535_T2.7011.00
188_V213_L2.6891.00
463_A466_Q2.6651.00
571_L576_P2.6471.00
411_L469_A2.6221.00
185_V217_R2.6181.00
522_A565_L2.5961.00
426_F446_Y2.5811.00
538_A557_L2.5751.00
1039_D1050_E2.5531.00
17_P225_W2.5501.00
95_I233_V2.5401.00
1106_V1111_N2.5111.00
608_Q612_N2.4591.00
512_E536_R2.4461.00
405_I459_V2.4371.00
950_T954_P2.4291.00
186_K190_M2.4271.00
954_P958_E2.4161.00
751_M767_F2.4101.00
170_M179_L2.3971.00
848_A866_E2.3971.00
98_A265_N2.3941.00
753_N757_R2.3821.00
371_M375_V2.3601.00
677_Q764_K2.3581.00
828_P882_E2.3551.00
187_E190_M2.3521.00
193_E197_T2.3491.00
702_I752_A2.2990.99
21_R230_V2.2910.99
635_E638_K2.2750.99
714_G718_K2.2640.99
1018_I1024_L2.2550.99
167_Q170_M2.2540.99
872_K875_E2.2470.99
851_Q863_N2.2450.99
717_M738_A2.2390.99
756_G759_I2.2270.99
466_Q470_R2.2190.99
139_P142_T2.2110.99
168_A177_K2.2070.99
1013_A1016_D2.1970.99
118_L121_S2.1820.99
1088_V1102_A2.1760.99
948_D951_Q2.1580.99
406_K429_T2.1450.99
481_N484_D2.1420.99
1039_D1043_V2.1290.99
627_I639_M2.1110.99
258_Y295_L2.0910.99
827_K883_E2.0880.99
481_N488_V2.0860.99
427_E470_R2.0760.99
607_A610_P2.0450.99
952_G955_R2.0290.99
425_A469_A2.0160.99
678_S682_N2.0140.99
658_V726_I2.0050.99
352_M475_A1.9990.99
170_M177_K1.9920.98
1009_R1026_E1.9790.98
361_M436_I1.9700.98
1068_E1071_V1.9660.98
197_T200_G1.9640.98
869_D873_A1.9620.98
657_T725_P1.9520.98
568_N572_P1.9470.98
35_N42_E1.9410.98
668_D671_E1.9380.98
444_T492_S1.9380.98
431_V437_R1.9360.98
847_F912_D1.9340.98
550_T553_Q1.9330.98
678_S681_D1.9290.98
78_C91_R1.9180.98
1102_A1106_V1.9180.98
28_V51_I1.9160.98
676_A708_A1.9120.98
136_V150_L1.9040.98
510_V535_T1.9000.98
1014_E1019_T1.8850.98
952_G958_E1.8850.98
479_I628_F1.8840.98
489_V640_L1.8820.98
272_L281_V1.8770.98
1048_L1071_V1.8770.98
19_K22_S1.8740.98
184_L187_E1.8700.98
30_K44_D1.8700.98
875_E879_A1.8660.98
899_C902_C1.8580.98
844_I870_E1.8530.98
1019_T1024_L1.8490.98
410_V428_P1.8460.97
1069_V1073_Q1.8410.97
1011_K1026_E1.8400.97
572_P576_P1.8330.97
299_G302_G1.8270.97
367_K466_Q1.8220.97
515_V538_A1.8190.97
674_E678_S1.8130.97
706_S710_D1.8070.97
988_Q993_V1.8020.97
195_L206_A1.7940.97
913_V917_E1.7850.97
549_F553_Q1.7830.97
75_C78_C1.7810.97
185_V189_D1.7800.97
854_H857_T1.7740.97
169_S177_K1.7670.97
340_G361_M1.7590.97
1030_D1033_E1.7590.97
360_E434_R1.7490.97
483_K767_F1.7330.96
703_S707_A1.7330.96
143_P162_Y1.7230.96
1078_V1116_G1.7200.96
960_F964_N1.7160.96
1018_I1022_Q1.7160.96
868_I873_A1.7150.96
849_R864_E1.7000.96
1043_V1050_E1.6980.96
816_T901_R1.6980.96
510_V532_H1.6970.96
635_E642_R1.6960.96
848_A851_Q1.6930.96
372_K376_E1.6880.96
820_T893_N1.6850.96
958_E964_N1.6830.96
101_V292_V1.6790.96
195_L200_G1.6740.96
526_Y562_V1.6700.95
685_K689_R1.6670.95
985_R988_Q1.6640.95
349_H437_R1.6600.95
848_A852_V1.6500.95
14_L106_Y1.6460.95
869_D879_A1.6400.95
840_E877_V1.6380.95
1052_Q1056_R1.6360.95
183_D189_D1.6330.95
351_K641_D1.6310.95
186_K189_D1.6260.95
165_K177_K1.6250.95
188_V217_R1.6230.95
984_V987_K1.6160.95
516_F531_V1.6140.95
865_N901_R1.6110.94
969_A972_T1.6050.94
1160_G1163_E1.6040.94
844_I905_R1.6020.94
176_H180_Q1.6000.94
382_N386_A1.6000.94
1050_E1056_R1.5840.94
565_L568_N1.5810.94
1019_T1022_Q1.5760.94
560_T565_L1.5750.94
867_L905_R1.5740.94
510_V513_G1.5730.94
15_A23_W1.5640.94
436_I457_V1.5610.93
604_A612_N1.5560.93
175_I179_L1.5460.93
840_E874_L1.5370.93
571_L575_F1.5370.93
469_A473_M1.5350.93
764_K775_E1.5330.93
168_A171_G1.5310.93
985_R993_V1.5270.93
848_A868_I1.5240.93
872_K876_I1.5200.93
442_V648_F1.5190.92
467_A471_I1.5170.92
1086_T1114_A1.5170.92
870_E905_R1.5160.92
352_M489_V1.5110.92
91_R118_L1.5100.92
632_H636_T1.5030.92
96_E230_V1.5000.92
605_V608_Q1.4950.92
990_E993_V1.4940.92
604_A610_P1.4910.92
973_E1036_K1.4890.92
503_T567_F1.4790.91
953_L958_E1.4790.91
813_I898_V1.4770.91
214_E217_R1.4750.91
999_T1002_Y1.4710.91
179_L183_D1.4690.91
102_S129_I1.4650.91
950_T955_R1.4630.91
512_E535_T1.4620.91
168_A173_E1.4450.90
1067_V1073_Q1.4450.90
992_V995_G1.4440.90
693_T696_E1.4410.90
903_Y908_A1.4370.90
563_G572_P1.4260.90
870_E879_A1.4190.90
673_L677_Q1.4190.90
340_G459_V1.4170.90
254_L316_L1.4090.89
973_E1000_R1.4070.89
228_L231_L1.4070.89
515_V557_L1.4040.89
1004_A1008_S1.4040.89
1023_V1029_I1.4040.89
1067_V1070_M1.4010.89
955_R959_L1.4000.89
29_K44_D1.3890.89
231_L296_I1.3880.89
168_A175_I1.3860.89
663_I726_I1.3840.88
671_E674_E1.3810.88
442_V475_A1.3810.88
71_K175_I1.3800.88
570_I576_P1.3780.88
698_Y757_R1.3730.88
85_A91_R1.3710.88
184_L213_L1.3700.88
1100_T1109_E1.3670.88
360_E393_V1.3630.88
1038_T1042_T1.3630.88
679_K707_A1.3610.88
181_D184_L1.3570.87
895_P1101_E1.3550.87
805_V921_I1.3540.87
180_Q222_K1.3530.87
1050_E1057_M1.3520.87
193_E198_S1.3510.87
1039_D1059_G1.3490.87
512_E516_F1.3490.87
177_K180_Q1.3480.87
868_I872_K1.3440.87
862_V872_K1.3440.87
866_E872_K1.3420.87
686_Q691_L1.3420.87
871_D875_E1.3400.87
366_F459_V1.3400.87
879_A883_E1.3400.87
1031_P1035_L1.3390.87
730_S741_F1.3380.87
972_T975_D1.3380.87
754_P781_H1.3350.87
1024_L1035_L1.3350.87
207_I211_E1.3350.87
531_V535_T1.3350.87
566_V650_Y1.3330.86
568_N571_L1.3330.86
1138_S1142_T1.3320.86
513_G516_F1.3230.86
371_M390_I1.3230.86
958_E965_P1.3220.86
1019_T1023_V1.3210.86
953_L961_E1.3200.86
957_Q962_A1.3190.86
753_N793_K1.3170.86
510_V514_M1.3140.86
952_G959_L1.3110.86
1040_L1050_E1.3100.86
629_K870_E1.3090.85
168_A179_L1.3090.85
898_V902_C1.3090.85
563_G566_V1.3090.85
175_I178_L1.3040.85
382_N389_K1.3010.85
860_V863_N1.2960.85
549_F552_E1.2940.85
151_S155_Y1.2920.85
373_E403_S1.2910.85
569_E572_P1.2900.85
649_K653_K1.2890.85
138_D141_N1.2890.85
493_Q608_Q1.2870.84
713_Q742_T1.2870.84
502_L566_V1.2820.84
607_A611_I1.2810.84
680_V701_V1.2800.84
955_R960_F1.2790.84
377_K403_S1.2780.84
148_Q154_E1.2730.84
315_S318_H1.2730.84
181_D186_K1.2710.84
1042_T1050_E1.2690.84
50_R659_G1.2640.83
1019_T1026_E1.2620.83
1023_V1026_E1.2620.83
607_A731_D1.2540.83
26_G51_I1.2530.83
117_V213_L1.2520.83
1027_G1030_D1.2490.83
1096_I1105_K1.2470.83
144_L158_Y1.2430.82
1033_E1036_K1.2430.82
234_I258_Y1.2430.82
859_E875_E1.2380.82
231_L875_E1.2370.82
1039_D1057_M1.2320.82
423_I469_A1.2310.82
877_V880_G1.2300.82
140_A143_P1.2300.82
699_E753_N1.2280.82
822_R893_N1.2260.81
987_K993_V1.2240.81
846_R851_Q1.2240.81
950_T958_E1.2200.81
850_K854_H1.2170.81
573_E576_P1.2160.81
608_Q611_I1.2110.81
846_R849_R1.2090.81
505_E536_R1.2070.80
574_S631_F1.2030.80
1039_D1045_E1.2010.80
985_R989_Q1.1990.80
548_T552_E1.1990.80
349_H645_N1.1980.80
748_R751_M1.1970.80
1045_E1050_E1.1970.80
265_N268_L1.1960.80
182_I185_V1.1930.80
526_Y533_L1.1930.80
354_Q427_E1.1910.79
155_Y168_A1.1900.79
627_I631_F1.1870.79
1168_G1174_G1.1860.79
1002_Y1018_I1.1860.79
604_A608_Q1.1860.79
1039_D1042_T1.1850.79
694_E697_R1.1830.79
113_R307_G1.1830.79
677_Q681_D1.1790.79
151_S156_R1.1780.79
1137_A1142_T1.1770.79
21_R229_D1.1770.79
135_V178_L1.1750.79
359_K432_E1.1740.79
194_E198_S1.1730.78
167_Q175_I1.1720.78
474_L477_Q1.1710.78
91_R121_S1.1710.78
1043_V1053_K1.1690.78
1050_E1053_K1.1660.78
953_L963_R1.1660.78
679_K704_I1.1660.78
514_M530_Y1.1650.78
117_V203_R1.1630.78
960_F963_R1.1610.78
117_V222_K1.1610.78
195_L198_S1.1600.78
422_G445_A1.1600.78
709_K713_Q1.1590.78
1059_G1062_I1.1590.78
958_E963_R1.1570.77
1030_D1034_L1.1570.77
1050_E1054_V1.1560.77
1045_E1049_H1.1560.77
1000_R1003_T1.1500.77
177_K184_L1.1470.77
145_E148_Q1.1470.77
954_P960_F1.1470.77
170_M178_L1.1470.77
854_H861_L1.1470.77
726_I744_L1.1460.77
873_A876_I1.1440.77
727_Y731_D1.1430.77
627_I765_S1.1430.77
472_L478_N1.1430.77
1044_Q1050_E1.1430.77
852_V861_L1.1420.77
370_V400_V1.1410.76
856_E867_L1.1400.76
531_V537_V1.1380.76
857_T861_L1.1360.76
755_A759_I1.1340.76
205_R405_I1.1320.76
1067_V1071_V1.1320.76
360_E488_V1.1280.76
566_V569_E1.1230.75
830_K833_T1.1200.75
551_E555_S1.1190.75
986_D993_V1.1170.75
102_S114_M1.1150.75
168_A172_A1.1130.75
1105_K1109_E1.1130.75
895_P898_V1.1130.75
901_R912_D1.1120.75
178_L182_I1.1120.75
966_K969_A1.1110.75
180_Q224_S1.1100.74
748_R779_S1.1090.74
565_L577_Y1.1090.74
951_Q955_R1.1090.74
185_V190_M1.1050.74
1045_E1056_R1.1040.74
876_I879_A1.1030.74
717_M767_F1.1030.74
797_S936_M1.1020.74
609_Q612_N1.1000.74
184_L190_M1.0990.74
871_D874_L1.0980.74
378_G551_E1.0970.74
709_K739_S1.0950.73
506_R665_V1.0950.73
848_A872_K1.0940.73
565_L570_I1.0940.73
1026_E1034_L1.0930.73
10_M13_G1.0920.73
953_L959_L1.0910.73
984_V989_Q1.0900.73
165_K175_I1.0880.73
956_I960_F1.0850.73
1014_E1024_L1.0850.73
1027_G1031_P1.0790.72
509_A535_T1.0790.72
1004_A1022_Q1.0750.72
165_K173_E1.0740.72
522_A562_V1.0740.72
754_P758_I1.0720.72
790_T938_T1.0710.72
1031_P1034_L1.0710.72
16_S225_W1.0690.72
714_G738_A1.0680.72
668_D711_V1.0680.72
950_T959_L1.0670.71
872_K879_A1.0640.71
854_H875_E1.0640.71
1066_H1071_V1.0640.71
773_V781_H1.0630.71
257_L260_R1.0630.71
405_I432_E1.0630.71
1058_Q1062_I1.0620.71
712_I746_G1.0620.71
1023_V1034_L1.0550.71
177_K182_I1.0550.71
611_I867_L1.0540.71
575_F631_F1.0520.70
626_E630_R1.0520.70
543_S551_E1.0510.70
172_A177_K1.0510.70
382_N387_K1.0500.70
632_H635_E1.0490.70
563_G568_N1.0470.70
755_A758_I1.0430.70
489_V495_M1.0420.70
137_T168_A1.0410.70
575_F627_I1.0380.69
869_D876_I1.0370.69
185_V188_V1.0360.69
1071_V1074_M1.0350.69
202_R1148_D1.0340.69
1010_L1016_D1.0250.68
541_A553_Q1.0230.68
682_N689_R1.0220.68
984_V993_V1.0220.68
1020_R1023_V1.0220.68
1107_L1113_P1.0200.68
270_R276_A1.0200.68
1125_K1140_Q1.0190.68
870_E873_A1.0170.68
834_E837_E1.0160.68
871_D876_I1.0150.68
184_L188_V1.0150.68
241_M382_N1.0140.68
1028_S1031_P1.0130.67
1020_R1029_I1.0130.67
121_S124_A1.0110.67
852_V862_V1.0090.67
767_F946_G1.0070.67
137_T167_Q1.0070.67
538_A556_K1.0050.67
78_C118_L1.0040.67
150_L155_Y1.0040.67
1168_G1175_T1.0030.67
856_E859_E1.0030.67
181_D185_V1.0020.67
15_A24_S1.0010.66
209_R212_V1.0000.66
1039_D1046_Y0.9960.66
528_N531_V0.9940.66
522_A526_Y0.9920.66
1039_D1056_R0.9900.66
380_A385_S0.9900.66
155_Y159_L0.9880.65
1060_V1068_E0.9880.65
692_I922_I0.9880.65
711_V714_G0.9850.65
625_A629_K0.9850.65
955_R962_A0.9830.65
72_G81_E0.9810.65
566_V570_I0.9800.65
508_G535_T0.9770.65
951_Q954_P0.9760.65
1014_E1018_I0.9760.65
1009_R1014_E0.9740.64
411_L446_Y0.9720.64
853_K861_L0.9680.64
196_K200_G0.9650.64
869_D874_L0.9620.63
182_I186_K0.9620.63
606_I639_M0.9600.63
952_G961_E0.9580.63
1015_G1022_Q0.9560.63
144_L148_Q0.9560.63
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504_L775_E0.5000.25
980_E984_V0.5000.25
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  
1hqmD 1 0.9016 100 0.199 Contact Map
4aybA 1 0.6756 100 0.361 Contact Map
4qiwA 2 0.6589 100 0.367 Contact Map
3qqcA 1 0.2619 100 0.77 Contact Map
4aybC 1 0.2611 100 0.827 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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