GREMLIN Database
RAPA - RNA polymerase-associated protein RapA
UniProt: P60240 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11083
Length: 968 (814)
Sequences: 2406 (1854)
Seq/√Len: 65.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
400_R404_V4.8231.00
143_P146_G4.4161.00
396_A400_R3.5541.00
131_R135_Y3.5121.00
411_H415_R3.2001.00
143_P147_L3.2001.00
142_M146_G3.1991.00
396_A404_V3.1321.00
131_R134_K3.0931.00
144_Y147_L2.9971.00
397_Q404_V2.9731.00
142_M145_S2.9061.00
397_Q400_R2.8641.00
132_A136_S2.8241.00
70_Q75_K2.8071.00
49_P52_R2.7911.00
498_L506_V2.7861.00
140_F143_P2.7261.00
129_R133_R2.7201.00
130_Y135_Y2.7101.00
133_R136_S2.7061.00
715_L718_F2.5321.00
219_M251_L2.5021.00
146_G149_G2.4771.00
133_R137_S2.4591.00
715_L720_M2.4571.00
67_W70_Q2.4521.00
78_N82_T2.3641.00
70_Q73_E2.3251.00
57_P61_I2.3131.00
52_R59_D2.3081.00
139_Q143_P2.2991.00
120_I123_M2.2921.00
48_S52_R2.2621.00
145_S148_R2.2421.00
715_L719_A2.2401.00
128_L133_R2.2311.00
141_R145_S2.1791.00
130_Y134_K2.1671.00
400_R403_L2.1581.00
141_R146_G2.1521.00
52_R57_P2.1381.00
84_I87_R2.1351.00
64_H68_Q2.1131.00
715_L722_L2.1081.00
80_L83_Y2.0961.00
139_Q144_Y2.0921.00
411_H414_S2.0801.00
47_D50_V2.0691.00
495_M527_E2.0681.00
77_E80_L2.0651.00
126_F129_R2.0611.00
49_P57_P2.0461.00
102_L107_V2.0391.00
63_S67_W2.0321.00
75_K78_N2.0061.00
129_R134_K2.0021.00
118_G121_D2.0011.00
134_K137_S1.9901.00
757_D760_T1.9821.00
51_T58_G1.9701.00
140_F146_G1.9571.00
96_A102_L1.9551.00
69_M74_V1.9541.00
74_V81_L1.9541.00
78_N81_L1.9451.00
132_A137_S1.9441.00
132_A135_Y1.9411.00
138_E143_P1.9381.00
59_D62_T1.9321.00
77_E81_L1.9281.00
83_Y87_R1.9081.00
52_R56_N1.9081.00
49_P61_I1.8901.00
65_D68_Q1.8881.00
780_E783_L1.8791.00
139_Q146_G1.8751.00
131_R137_S1.8701.00
81_L85_G1.8681.00
800_T803_L1.8641.00
886_A891_G1.8621.00
128_L131_R1.8541.00
125_R129_R1.8481.00
70_Q74_V1.8471.00
53_V56_N1.8451.00
404_V407_L1.8441.00
56_N61_I1.8421.00
68_Q73_E1.8321.00
130_Y133_R1.8291.00
79_G83_Y1.8181.00
714_N718_F1.8171.00
58_G61_I1.8131.00
69_M75_K1.8081.00
140_F144_Y1.8021.00
64_H67_W1.7991.00
68_Q72_E1.7981.00
714_N717_A1.7971.00
138_E142_M1.7941.00
70_Q81_L1.7871.00
69_M72_E1.7841.00
67_W75_K1.7791.00
400_R409_D1.7771.00
129_R135_Y1.7761.00
131_R136_S1.7751.00
168_R173_V1.7701.00
130_Y137_S1.7691.00
119_Q122_R1.7601.00
82_T85_G1.7571.00
50_V60_T1.7461.00
53_V58_G1.7461.00
102_L106_L1.7411.00
716_I721_N1.7351.00
51_T54_M1.7341.00
48_S53_V1.7250.99
79_G84_I1.7240.99
49_P60_T1.7200.99
143_P148_R1.7140.99
140_F145_S1.7100.99
142_M147_L1.7070.99
404_V409_D1.6980.99
76_E79_G1.6950.99
71_V74_V1.6900.99
56_N60_T1.6880.99
69_M73_E1.6830.99
50_V59_D1.6720.99
80_L84_I1.6480.99
139_Q145_S1.6480.99
68_Q79_G1.6400.99
52_R61_I1.6320.99
139_Q142_M1.6310.99
412_G415_R1.6240.99
52_R55_F1.6190.99
50_V53_V1.6180.99
50_V57_P1.6150.99
57_P60_T1.6120.99
791_I796_T1.6080.99
758_G762_T1.6060.99
50_V61_I1.6050.99
400_R407_L1.6010.99
74_V77_E1.5960.99
47_D52_R1.5910.99
776_F779_W1.5840.99
100_V107_V1.5830.99
775_Q779_W1.5820.99
895_I898_S1.5770.99
49_P56_N1.5690.99
51_T61_I1.5660.99
382_I386_L1.5660.99
74_V78_N1.5650.99
54_M57_P1.5630.99
53_V61_I1.5620.99
55_F59_D1.5530.99
64_H72_E1.5530.99
409_D415_R1.5500.99
117_A123_M1.5480.99
138_E145_S1.5450.99
53_V57_P1.5450.99
52_R58_G1.5430.99
520_E531_A1.5400.99
410_R415_R1.5390.99
71_V84_I1.5380.99
765_R768_A1.5360.99
61_I68_Q1.5330.99
47_D54_M1.5290.99
782_P789_D1.5250.99
807_K810_P1.5220.99
48_S51_T1.5210.99
97_L102_L1.5190.99
117_A120_I1.5180.99
48_S60_T1.5160.99
128_L137_S1.5130.99
77_E82_T1.5020.99
70_Q77_E1.4990.99
127_A133_R1.4980.99
54_M58_G1.4940.99
97_L106_L1.4930.99
49_P54_M1.4900.98
232_D262_S1.4860.98
383_E386_L1.4850.98
96_A106_L1.4840.98
70_Q78_N1.4830.98
494_L579_V1.4790.98
113_D117_A1.4750.98
64_H69_M1.4730.98
54_M61_I1.4710.98
67_W71_V1.4620.98
128_L134_K1.4590.98
67_W73_E1.4570.98
405_S409_D1.4460.98
750_D755_S1.4460.98
719_A724_D1.4450.98
129_R136_S1.4440.98
396_A406_M1.4430.98
63_S68_Q1.4410.98
125_R131_R1.4370.98
398_S404_V1.4320.98
129_R132_A1.4230.98
48_S54_M1.4220.98
73_E79_G1.4170.98
87_R90_T1.4140.98
224_N227_F1.4090.98
714_N719_A1.4080.98
72_E75_K1.4060.98
718_F722_L1.4010.98
418_F421_T1.3950.98
718_F723_F1.3940.98
67_W74_V1.3870.98
57_P68_Q1.3860.98
79_G82_T1.3830.98
632_F637_P1.3830.98
623_R627_E1.3820.98
821_V826_A1.3800.97
703_A707_E1.3770.97
79_G87_R1.3770.97
56_N59_D1.3760.97
716_I719_A1.3740.97
140_F147_L1.3730.97
185_I188_G1.3720.97
50_V58_G1.3680.97
400_R413_T1.3680.97
845_L849_G1.3670.97
81_L84_I1.3670.97
112_Q117_A1.3670.97
99_E102_L1.3660.97
750_D753_G1.3650.97
66_G69_M1.3650.97
139_Q147_L1.3640.97
145_S149_G1.3550.97
787_G790_L1.3550.97
65_D70_Q1.3530.97
70_Q84_I1.3420.97
66_G70_Q1.3360.97
60_T64_H1.3260.97
50_V55_F1.3260.97
64_H73_E1.3220.97
96_A107_V1.3220.97
78_N89_D1.3200.97
125_R132_A1.3160.97
49_P59_D1.3040.96
228_A232_D1.3030.96
47_D61_I1.3000.96
396_A405_S1.2960.96
51_T56_N1.2930.96
112_Q116_F1.2920.96
67_W79_G1.2880.96
77_E84_I1.2860.96
79_G88_L1.2810.96
75_K81_L1.2810.96
783_L786_N1.2790.96
51_T59_D1.2790.96
125_R128_L1.2780.96
719_A723_F1.2770.96
72_E79_G1.2760.96
116_F119_Q1.2750.96
875_K879_A1.2730.96
719_A722_L1.2730.96
63_S73_E1.2710.96
495_M522_V1.2700.96
96_A100_V1.2690.96
779_W783_L1.2670.96
47_D57_P1.2660.96
63_S66_G1.2640.96
739_V742_P1.2610.96
49_P66_G1.2610.96
59_D71_V1.2590.96
56_N67_W1.2530.96
779_W782_P1.2510.95
54_M59_D1.2490.95
51_T63_S1.2490.95
721_N725_I1.2490.95
74_V79_G1.2470.95
62_T66_G1.2470.95
58_G62_T1.2460.95
836_L840_P1.2460.95
48_S58_G1.2450.95
48_S57_P1.2430.95
127_A134_K1.2400.95
127_A131_R1.2370.95
73_E76_E1.2350.95
68_Q75_K1.2350.95
767_V771_R1.2320.95
50_V56_N1.2300.95
826_A830_L1.2300.95
66_G71_V1.2290.95
116_F120_I1.2280.95
59_D66_G1.2270.95
746_M753_G1.2260.95
881_Q885_H1.2260.95
698_K702_L1.2260.95
504_Q576_S1.2250.95
782_P787_G1.2220.95
100_V108_F1.2220.95
63_S79_G1.2200.95
400_R405_S1.2200.95
141_R144_Y1.2180.95
786_N793_S1.2170.95
845_L848_N1.2150.95
409_D413_T1.2130.95
126_F131_R1.2090.95
746_M750_D1.2070.95
117_A121_D1.2000.94
65_D69_M1.1990.94
887_I891_G1.1980.94
65_D75_K1.1980.94
822_V826_A1.1970.94
112_Q122_R1.1960.94
63_S81_L1.1930.94
115_L121_D1.1900.94
51_T60_T1.1890.94
401_Q404_V1.1850.94
79_G86_T1.1830.94
409_D414_S1.1810.94
712_D715_L1.1810.94
739_V745_H1.1800.94
97_L107_V1.1790.94
786_N790_L1.1780.94
706_I709_Q1.1780.94
49_P53_V1.1760.94
782_P785_R1.1710.94
225_L229_L1.1710.94
858_F861_F1.1700.94
717_A720_M1.1690.94
714_N723_F1.1660.93
746_M749_P1.1660.93
403_L409_D1.1650.93
126_F133_R1.1640.93
52_R60_T1.1630.93
715_L723_F1.1630.93
83_Y88_L1.1630.93
781_H784_I1.1600.93
68_Q71_V1.1590.93
96_A108_F1.1530.93
411_H417_L1.1520.93
419_R422_R1.1500.93
48_S61_I1.1480.93
130_Y136_S1.1480.93
70_Q86_T1.1450.93
71_V76_E1.1440.93
50_V54_M1.1430.93
53_V72_E1.1410.93
66_G74_V1.1400.93
883_D887_I1.1390.93
67_W72_E1.1380.93
418_F422_R1.1350.93
48_S59_D1.1350.93
396_A401_Q1.1350.93
102_L108_F1.1340.92
66_G79_G1.1330.92
870_R873_G1.1310.92
114_R117_A1.1280.92
77_E83_Y1.1270.92
788_L791_I1.1230.92
784_I788_L1.1220.92
846_D849_G1.1210.92
888_L891_G1.1170.92
85_G89_D1.1150.92
227_F232_D1.1130.92
55_F58_G1.1090.92
751_F754_L1.1080.92
523_L558_Q1.1080.92
88_L95_V1.1070.92
63_S75_K1.1040.91
760_T765_R1.1030.91
778_T782_P1.1020.91
63_S71_V1.1010.91
113_D119_Q1.1000.91
75_K84_I1.0970.91
75_K89_D1.0960.91
48_S56_N1.0960.91
47_D59_D1.0950.91
747_L754_L1.0950.91
81_L89_D1.0920.91
766_E769_L1.0900.91
899_A905_A1.0890.91
783_L794_G1.0890.91
813_T821_V1.0880.91
901_A905_A1.0820.91
741_T744_D1.0800.91
71_V77_E1.0770.90
801_I807_K1.0750.90
51_T55_F1.0750.90
441_P444_Y1.0740.90
77_E85_G1.0740.90
905_A910_A1.0730.90
97_L100_V1.0730.90
112_Q115_L1.0730.90
48_S55_F1.0720.90
75_K85_G1.0720.90
693_S697_E1.0700.90
63_S78_N1.0690.90
396_A409_D1.0690.90
396_A407_L1.0680.90
651_I655_A1.0680.90
206_I299_I1.0670.90
71_V75_K1.0660.90
54_M60_T1.0650.90
78_N85_G1.0630.90
404_V413_T1.0610.90
67_W84_I1.0590.90
397_Q403_L1.0580.90
715_L724_D1.0560.90
55_F60_T1.0550.89
779_W787_G1.0510.89
784_I792_L1.0500.89
70_Q90_T1.0460.89
396_A403_L1.0460.89
784_I787_G1.0460.89
714_N720_M1.0450.89
821_V827_P1.0410.89
71_V81_L1.0410.89
856_V860_T1.0390.89
65_D73_E1.0390.89
113_D122_R1.0380.89
836_L839_T1.0380.89
765_R769_L1.0370.89
67_W77_E1.0360.89
47_D55_F1.0350.89
51_T65_D1.0350.89
128_L132_A1.0340.88
836_L848_N1.0340.88
783_L787_G1.0340.88
121_D124_D1.0320.88
699_A702_L1.0310.88
111_P114_R1.0290.88
73_E77_E1.0280.88
56_N62_T1.0250.88
227_F230_F1.0240.88
55_F61_I1.0220.88
78_N86_T1.0170.88
653_Y656_S1.0160.88
713_T723_F1.0160.88
814_L824_A1.0160.88
818_L821_V1.0150.88
806_N809_L1.0120.87
810_P813_T1.0110.87
138_E146_G1.0100.87
83_Y89_D1.0100.87
128_L135_Y1.0080.87
857_E860_T1.0070.87
59_D65_D1.0060.87
83_Y86_T1.0050.87
112_Q119_Q1.0050.87
51_T62_T1.0040.87
842_R849_G1.0030.87
60_T73_E1.0020.87
62_T65_D1.0010.87
908_N912_E1.0010.87
57_P62_T1.0000.87
53_V60_T0.9980.87
821_V828_K0.9930.86
399_A404_V0.9930.86
49_P58_G0.9920.86
406_M409_D0.9910.86
102_L105_K0.9900.86
718_F721_N0.9900.86
820_Y823_E0.9890.86
172_R331_L0.9890.86
63_S69_M0.9890.86
716_I720_M0.9880.86
703_A710_D0.9880.86
887_I890_L0.9860.86
532_A556_G0.9840.86
61_I67_W0.9830.86
138_E147_L0.9830.86
398_S409_D0.9820.86
414_S417_L0.9810.86
127_A130_Y0.9810.86
74_V85_G0.9800.86
115_L118_G0.9800.86
68_Q90_T0.9790.86
836_L849_G0.9790.86
783_L789_D0.9780.86
82_T90_T0.9780.86
57_P71_V0.9760.85
66_G72_E0.9760.85
807_K811_V0.9740.85
398_S401_Q0.9730.85
234_R239_Q0.9710.85
66_G75_K0.9700.85
423_N426_K0.9700.85
775_Q788_L0.9690.85
806_N815_L0.9690.85
70_Q76_E0.9670.85
779_W784_I0.9670.85
886_A890_L0.9660.85
72_E77_E0.9650.85
53_V64_H0.9640.85
52_R65_D0.9640.85
60_T65_D0.9640.85
848_N852_L0.9620.85
217_V548_A0.9610.85
56_N63_S0.9590.84
778_T785_R0.9570.84
125_R133_R0.9560.84
840_P849_G0.9550.84
761_I765_R0.9540.84
403_L407_L0.9540.84
409_D412_G0.9540.84
73_E78_N0.9530.84
62_T77_E0.9520.84
86_T89_D0.9510.84
905_A911_D0.9510.84
779_W792_L0.9510.84
811_V818_L0.9500.84
68_Q74_V0.9500.84
47_D53_V0.9500.84
764_D768_A0.9500.84
84_I88_L0.9490.84
112_Q118_G0.9480.84
379_E386_L0.9470.84
48_S63_S0.9460.84
86_T90_T0.9440.83
76_E86_T0.9430.83
891_G895_I0.9430.83
47_D60_T0.9430.83
82_T86_T0.9420.83
113_D116_F0.9410.83
407_L415_R0.9410.83
80_L88_L0.9400.83
815_L818_L0.9390.83
834_R840_P0.9380.83
778_T781_H0.9340.83
111_P115_L0.9340.83
797_G800_T0.9310.83
763_F767_V0.9270.82
583_L625_Y0.9260.82
71_V79_G0.9250.82
70_Q83_Y0.9250.82
773_D776_F0.9250.82
76_E81_L0.9240.82
52_R63_S0.9230.82
57_P74_V0.9190.82
224_N228_A0.9180.82
59_D72_E0.9160.82
797_G803_L0.9150.82
840_P855_Q0.9150.82
49_P63_S0.9140.81
64_H79_G0.9140.81
713_T719_A0.9120.81
779_W788_L0.9090.81
712_D716_I0.9090.81
712_D718_F0.9090.81
401_Q405_S0.9070.81
762_T765_R0.9070.81
855_Q858_F0.9060.81
823_E826_A0.9060.81
817_E830_L0.9050.81
739_V750_D0.9040.81
781_H786_N0.9040.81
905_A909_E0.9020.81
909_E913_K0.9020.81
54_M64_H0.9020.81
781_H787_G0.9010.81
677_L680_Q0.9010.81
78_N84_I0.8990.80
58_G75_K0.8970.80
400_R406_M0.8930.80
398_S406_M0.8920.80
51_T57_P0.8920.80
844_L848_N0.8920.80
759_I763_F0.8910.80
654_L657_P0.8910.80
749_P753_G0.8880.80
839_T842_R0.8870.79
61_I71_V0.8870.79
779_W786_N0.8860.79
58_G66_G0.8840.79
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855_Q872_T0.5340.43
782_P792_L0.5330.43
56_N71_V0.5330.43
67_W85_G0.5320.42
676_A685_R0.5320.42
860_T866_N0.5310.42
785_R790_L0.5300.42
64_H74_V0.5300.42
398_S403_L0.5300.42
806_N821_V0.5290.42
52_R70_Q0.5290.42
75_K83_Y0.5280.42
809_L812_G0.5280.42
79_G90_T0.5280.42
59_D83_Y0.5280.42
856_V861_F0.5280.42
807_K821_V0.5270.42
56_N78_N0.5270.42
59_D73_E0.5260.42
61_I76_E0.5260.42
790_L794_G0.5260.42
777_I782_P0.5260.42
791_I798_S0.5240.41
903_I912_E0.5240.41
858_F869_N0.5240.41
845_L855_Q0.5230.41
713_T724_D0.5230.41
882_Q893_A0.5230.41
785_R788_L0.5220.41
396_A616_T0.5210.41
812_G818_L0.5190.41
906_A913_K0.5180.41
898_S907_R0.5180.41
890_L894_Q0.5170.41
717_A722_L0.5170.41
325_F338_D0.5170.41
53_V69_M0.5150.40
52_R64_H0.5150.40
810_P815_L0.5150.40
58_G72_E0.5150.40
650_L657_P0.5150.40
759_I771_R0.5140.40
76_E89_D0.5140.40
898_S906_A0.5140.40
488_D581_F0.5130.40
832_L836_L0.5130.40
737_M741_T0.5130.40
783_L793_S0.5130.40
727_G730_Q0.5120.40
772_E783_L0.5110.40
398_S413_T0.5110.40
782_P798_S0.5110.40
69_M83_Y0.5110.40
850_N859_E0.5100.40
65_D74_V0.5100.40
856_V859_E0.5100.40
901_A906_A0.5090.40
758_G763_F0.5090.40
881_Q888_L0.5080.40
861_F864_Q0.5080.40
61_I72_E0.5070.40
906_A915_S0.5070.40
855_Q873_G0.5060.39
887_I892_E0.5060.39
142_M148_R0.5060.39
61_I84_I0.5060.39
811_V822_V0.5060.39
825_Q828_K0.5040.39
772_E776_F0.5040.39
126_F132_A0.5040.39
529_I557_A0.5030.39
809_L814_L0.5030.39
384_P389_A0.5030.39
788_L796_T0.5020.39
50_V63_S0.5020.39
892_E900_R0.5020.39
98_R108_F0.5020.39
58_G67_W0.5010.39
716_I723_F0.5010.39
910_A915_S0.5000.39
875_K878_N0.5000.39
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  
3mwyW 2 0.6498 100 0.478 Contact Map
3dmqA 1 0.9886 100 0.491 Contact Map
1z3iX 4 0.6198 100 0.528 Contact Map
1z63A 1 0.4628 100 0.55 Contact Map
2ykgA 1 0.5919 100 0.675 Contact Map
4a2qA 1 0.5579 100 0.681 Contact Map
1wp9A 1 0.4752 100 0.69 Contact Map
4a2wA 1 0.5527 100 0.692 Contact Map
4a2pA 1 0.4463 100 0.718 Contact Map
3tbkA 1 0.4855 100 0.72 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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