GREMLIN Database
RPOA2 - DNA-directed RNA polymerase subunit A''
UniProt: P0CX07 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 397 (347)
Sequences: 2397 (1470)
Seq/√Len: 78.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
157_V161_L3.6211.00
102_E106_A3.3821.00
116_E119_L3.0971.00
154_D162_N2.9061.00
153_A157_V2.7351.00
98_P102_E2.7021.00
191_L197_Q2.6981.00
103_L292_I2.6851.00
92_D95_Q2.5561.00
191_L195_V2.5011.00
188_E191_L2.4881.00
154_D157_V2.4791.00
175_S178_Q2.4761.00
166_L172_R2.4091.00
166_L171_P2.3381.00
117_V120_E2.2981.00
35_G44_I2.2961.00
287_A290_E2.2951.00
114_V119_L2.1791.00
279_V291_A2.1521.00
187_I194_T2.1391.00
116_E120_E2.0971.00
153_A161_L2.0201.00
102_E108_K2.0071.00
156_V162_N2.0021.00
126_E129_R1.9521.00
101_I147_D1.9361.00
154_D159_I1.9041.00
115_M120_E1.8901.00
187_I190_N1.8711.00
297_M301_E1.8631.00
47_A56_R1.8591.00
191_L198_D1.8511.00
172_R178_Q1.8471.00
147_D150_T1.8401.00
113_P116_E1.8031.00
157_V163_E1.7951.00
154_D161_L1.7951.00
170_W178_Q1.7931.00
189_G195_V1.7841.00
157_V162_N1.7781.00
172_R176_T1.7681.00
166_L174_D1.7621.00
294_N298_T1.7571.00
188_E194_T1.7271.00
144_A150_T1.7251.00
193_V196_T1.7121.00
98_P104_V1.7071.00
113_P117_V1.7041.00
96_G99_R1.6831.00
104_V108_K1.6781.00
186_T190_N1.6761.00
190_N197_Q1.6751.00
172_R177_T1.6661.00
290_E294_N1.6651.00
42_N367_D1.6601.00
99_R102_E1.6461.00
192_G196_T1.6381.00
192_G195_V1.6371.00
171_P174_D1.6341.00
119_L122_E1.6171.00
174_D177_T1.6011.00
193_V197_Q1.5961.00
267_D270_R1.5851.00
97_L102_E1.5660.99
368_G371_E1.5630.99
141_K144_A1.5590.99
162_N166_L1.5520.99
153_A162_N1.4960.99
176_T179_I1.4940.99
187_I193_V1.4850.99
153_A159_I1.4790.99
190_N199_G1.4750.99
166_L176_T1.4710.99
169_R172_R1.4710.99
169_R177_T1.4700.99
166_L170_W1.4690.99
157_V160_D1.4620.99
356_D360_H1.4580.99
153_A156_V1.4480.99
170_W177_T1.4450.99
196_T200_T1.4360.99
372_N377_K1.4340.99
156_V160_D1.4270.99
186_T189_G1.4230.99
190_N193_V1.4230.99
166_L169_R1.4210.99
169_R175_S1.4140.99
191_L194_T1.4120.99
169_R178_Q1.4100.99
154_D163_E1.3960.99
187_I196_T1.3880.99
188_E193_V1.3870.99
189_G194_T1.3850.99
98_P106_A1.3790.99
99_R105_D1.3790.99
112_T115_M1.3780.99
191_L200_T1.3750.99
103_L106_A1.3700.99
283_L287_A1.3670.99
103_L145_L1.3600.99
104_V140_T1.3500.98
190_N194_T1.3490.98
99_R108_K1.3480.98
101_I104_V1.3470.98
170_W176_T1.3460.98
171_P175_S1.3420.98
116_E122_E1.3400.98
57_V61_D1.3360.98
113_P119_L1.3340.98
188_E195_V1.3120.98
169_R176_T1.3010.98
170_W180_A1.3000.98
186_T192_G1.2970.98
175_S179_I1.2920.98
187_I199_G1.2830.98
188_E196_T1.2790.98
112_T119_L1.2750.98
188_E197_Q1.2740.98
194_T198_D1.2730.98
284_G287_A1.2640.98
147_D160_D1.2570.98
187_I191_L1.2570.98
32_E35_G1.2410.97
190_N195_V1.2400.97
102_E110_P1.2380.97
133_V136_K1.2280.97
154_D160_D1.2200.97
292_I324_G1.2170.97
168_E171_P1.2140.97
238_R249_V1.2130.97
186_T191_L1.2060.97
99_R104_V1.2060.97
297_M308_V1.2030.97
194_T199_G1.1900.97
171_P179_I1.1890.97
170_W175_S1.1870.97
175_S180_A1.1860.97
214_L218_V1.1800.96
177_T180_A1.1790.96
167_Q175_S1.1720.96
169_R180_A1.1670.96
256_A259_K1.1650.96
171_P178_Q1.1630.96
98_P101_I1.1540.96
110_P113_P1.1480.96
292_I296_T1.1450.96
350_T357_A1.1430.96
172_R180_A1.1410.96
173_V178_Q1.1380.96
167_Q178_Q1.1340.96
156_V163_E1.1300.95
155_M161_L1.1280.95
191_L196_T1.1260.95
168_E175_S1.1210.95
97_L104_V1.1180.95
176_T180_A1.1180.95
186_T195_V1.1080.95
372_N380_R1.1050.95
172_R175_S1.1000.95
112_T120_E1.0960.95
242_T249_V1.0940.95
190_N196_T1.0770.94
296_T385_D1.0750.94
97_L105_D1.0720.94
196_T199_G1.0700.94
192_G198_D1.0670.94
117_V121_D1.0600.94
174_D178_Q1.0580.94
225_V230_E1.0550.93
190_N198_D1.0530.93
94_T99_R1.0520.93
345_A350_T1.0520.93
260_A266_V1.0440.93
330_G371_E1.0430.93
112_T116_E1.0430.93
133_V283_L1.0400.93
45_A48_V1.0360.93
88_V91_M1.0360.93
159_I162_N1.0330.93
187_I192_G1.0310.93
114_V123_Y1.0280.93
100_L104_V1.0190.92
189_G198_D1.0170.92
194_T197_Q1.0160.92
167_Q172_R1.0110.92
75_G329_I1.0100.92
344_R362_E1.0070.92
145_L226_F1.0010.92
187_I198_D1.0000.91
186_T197_Q0.9970.91
111_D115_M0.9960.91
71_I75_G0.9950.91
300_L305_L0.9940.91
115_M121_D0.9940.91
174_D179_I0.9930.91
166_L175_S0.9890.91
172_R179_I0.9850.91
168_E172_R0.9840.91
166_L178_Q0.9800.91
163_E166_L0.9800.91
168_E178_Q0.9770.91
156_V161_L0.9740.90
97_L107_R0.9720.90
334_I343_A0.9720.90
45_A50_A0.9690.90
115_M119_L0.9670.90
342_L373_V0.9610.90
186_T194_T0.9600.90
80_M288_A0.9590.90
189_G192_G0.9550.89
213_E216_Q0.9510.89
80_M222_R0.9500.89
153_A168_E0.9440.89
171_P180_A0.9400.89
79_T82_T0.9370.89
99_R110_P0.9370.89
236_V253_E0.9350.88
272_S291_A0.9310.88
63_V315_L0.9280.88
181_G186_T0.9280.88
319_I343_A0.9280.88
55_T58_D0.9250.88
113_P122_E0.9240.88
160_D163_E0.9230.88
316_V352_N0.9230.88
296_T322_N0.9200.88
284_G288_A0.9200.88
96_G102_E0.9170.88
36_V264_E0.9150.87
119_L123_Y0.9090.87
254_G289_R0.9070.87
129_R132_E0.9010.87
33_E38_K0.9010.87
272_S294_N0.9000.87
192_G197_Q0.8990.86
95_Q100_L0.8970.86
268_A282_T0.8970.86
189_G197_Q0.8960.86
173_V179_I0.8920.86
132_E136_K0.8920.86
200_T210_S0.8910.86
94_T97_L0.8900.86
101_I106_A0.8840.86
116_E121_D0.8810.85
170_W179_I0.8810.85
177_T181_G0.8760.85
101_I105_D0.8750.85
102_E109_T0.8720.85
105_D108_K0.8720.85
99_R106_A0.8690.85
173_V176_T0.8680.84
346_A350_T0.8650.84
104_V152_V0.8620.84
96_G106_A0.8610.84
98_P108_K0.8590.84
163_E167_Q0.8590.84
162_N174_D0.8580.84
100_L108_K0.8570.84
158_R162_N0.8560.84
102_E105_D0.8510.83
96_G103_L0.8500.83
286_E388_L0.8460.83
94_T100_L0.8450.83
102_E107_R0.8440.83
38_K45_A0.8410.83
98_P103_L0.8320.82
292_I317_A0.8300.82
107_R110_P0.8300.82
120_E123_Y0.8290.82
195_V198_D0.8270.81
277_H280_H0.8250.81
191_L199_G0.8250.81
214_L217_L0.8240.81
161_L166_L0.8230.81
188_E200_T0.8220.81
104_V107_R0.8130.80
85_Y88_V0.8100.80
106_A109_T0.8090.80
64_G76_T0.8090.80
310_I314_M0.8090.80
233_S298_T0.8080.80
96_G286_E0.8080.80
195_V199_G0.8020.79
102_E112_T0.7990.79
167_Q179_I0.7990.79
167_Q171_P0.7970.79
197_Q200_T0.7960.79
310_I332_H0.7950.79
187_I197_Q0.7930.79
167_Q176_T0.7930.79
192_G199_G0.7930.79
343_A373_V0.7920.79
47_A296_T0.7920.79
162_N179_I0.7900.78
140_T144_A0.7890.78
358_A368_G0.7860.78
286_E295_E0.7820.78
159_I163_E0.7820.78
96_G100_L0.7760.77
293_I317_A0.7750.77
104_V109_T0.7660.76
95_Q102_E0.7630.76
248_F281_K0.7600.76
188_E192_G0.7580.76
38_K50_A0.7580.76
36_V324_G0.7570.75
154_D168_E0.7520.75
93_V286_E0.7510.75
97_L106_A0.7510.75
120_E265_G0.7510.75
168_E176_T0.7500.75
273_C324_G0.7440.74
154_D158_R0.7430.74
212_R215_L0.7430.74
115_M122_E0.7410.74
194_T200_T0.7400.74
181_G195_V0.7380.74
187_I200_T0.7380.74
97_L103_L0.7380.74
328_S354_L0.7360.73
153_A163_E0.7330.73
80_M331_R0.7330.73
155_M163_E0.7290.73
173_V177_T0.7250.72
211_Y214_L0.7220.72
105_D330_G0.7210.72
100_L292_I0.7200.72
186_T193_V0.7160.71
65_T292_I0.7120.71
186_T196_T0.7090.71
297_M310_I0.7080.70
52_Y289_R0.7070.70
99_R107_R0.7050.70
294_N326_I0.7040.70
108_K112_T0.7040.70
65_T316_V0.7030.70
85_Y302_E0.7010.70
119_L130_A0.6970.69
187_I195_V0.6970.69
330_G380_R0.6960.69
112_T117_V0.6960.69
97_L100_L0.6940.69
103_L113_P0.6930.69
51_Q54_D0.6910.69
234_R253_E0.6900.68
171_P176_T0.6860.68
167_Q170_W0.6810.67
186_T198_D0.6790.67
170_W174_D0.6780.67
67_S316_V0.6780.67
190_N210_S0.6770.67
243_E265_G0.6770.67
43_E46_T0.6750.67
234_R238_R0.6740.67
101_I107_R0.6730.67
113_P120_E0.6700.66
81_N379_V0.6680.66
75_G81_N0.6680.66
189_G196_T0.6680.66
103_L107_R0.6660.66
350_T374_I0.6650.66
49_E380_R0.6630.65
228_G345_A0.6620.65
211_Y215_L0.6620.65
64_G77_Q0.6610.65
81_N300_L0.6590.65
368_G372_N0.6560.65
94_T113_P0.6560.65
166_L180_A0.6550.64
94_T102_E0.6550.64
257_F324_G0.6540.64
300_L303_Q0.6540.64
67_S312_H0.6520.64
213_E218_V0.6520.64
329_I350_T0.6500.64
171_P177_T0.6500.64
230_E238_R0.6480.64
241_E269_T0.6470.64
27_V145_L0.6460.63
252_T331_R0.6440.63
322_N339_N0.6440.63
268_A271_T0.6410.63
92_D96_G0.6410.63
297_M313_L0.6400.63
125_E129_R0.6400.63
169_R174_D0.6380.62
99_R295_E0.6370.62
169_R173_V0.6360.62
106_A110_P0.6360.62
99_R287_A0.6360.62
109_T112_T0.6350.62
271_T324_G0.6330.62
261_L265_G0.6330.62
376_G382_G0.6310.62
93_V96_G0.6310.62
255_S282_T0.6310.62
250_L273_C0.6290.61
326_I330_G0.6280.61
153_A178_Q0.6270.61
283_L286_E0.6260.61
57_V118_Y0.6260.61
94_T106_A0.6220.61
320_M329_I0.6200.60
374_I379_V0.6180.60
190_N200_T0.6170.60
343_A370_I0.6150.60
36_V250_L0.6150.60
285_I321_T0.6150.60
157_V166_L0.6130.59
195_V200_T0.6110.59
59_P286_E0.6100.59
275_N283_L0.6090.59
230_E301_E0.6070.59
354_L371_E0.6040.58
114_V327_E0.6030.58
138_E144_A0.6020.58
359_I375_V0.6010.58
276_I288_A0.6000.58
167_Q174_D0.5990.58
110_P119_L0.5980.58
75_G371_E0.5960.57
29_A151_N0.5950.57
259_K274_N0.5950.57
181_G193_V0.5930.57
55_T63_V0.5930.57
274_N286_E0.5920.57
168_E181_G0.5920.57
281_K323_D0.5900.57
161_L167_Q0.5890.56
45_A49_E0.5880.56
99_R243_E0.5870.56
240_E249_V0.5870.56
345_A353_H0.5850.56
97_L101_I0.5840.56
293_I375_V0.5790.55
181_G188_E0.5790.55
385_D388_L0.5780.55
239_R246_E0.5770.55
168_E177_T0.5770.55
38_K49_E0.5740.54
61_D303_Q0.5740.54
59_P386_V0.5740.54
117_V122_E0.5720.54
349_V369_V0.5720.54
247_E289_R0.5720.54
169_R179_I0.5670.54
100_L113_P0.5660.53
239_R301_E0.5650.53
71_I269_T0.5640.53
193_V199_G0.5640.53
88_V292_I0.5640.53
66_V272_S0.5610.53
300_L353_H0.5600.53
366_L375_V0.5600.53
160_D178_Q0.5580.52
38_K43_E0.5580.52
41_A105_D0.5580.52
160_D167_Q0.5560.52
145_L171_P0.5560.52
51_Q309_N0.5540.52
257_F261_L0.5540.52
294_N360_H0.5510.52
58_D65_T0.5510.52
44_I48_V0.5510.52
162_N169_R0.5510.52
273_C356_D0.5480.51
38_K42_N0.5460.51
213_E220_Q0.5460.51
155_M159_I0.5450.51
189_G193_V0.5440.51
47_A51_Q0.5440.51
349_V352_N0.5430.50
261_L271_T0.5430.50
96_G112_T0.5430.50
181_G191_L0.5430.50
113_P121_D0.5420.50
79_T94_T0.5410.50
27_V32_E0.5390.50
158_R173_V0.5390.50
192_G200_T0.5370.50
157_V170_W0.5360.50
116_E123_Y0.5360.50
74_P78_M0.5320.49
233_S242_T0.5290.49
134_V334_I0.5290.49
156_V167_Q0.5290.49
115_M252_T0.5270.48
27_V31_A0.5260.48
162_N168_E0.5250.48
305_L313_L0.5250.48
181_G194_T0.5240.48
329_I371_E0.5240.48
96_G109_T0.5230.48
53_L377_K0.5220.48
95_Q105_D0.5210.48
224_I236_V0.5200.48
173_V199_G0.5180.47
125_E128_E0.5160.47
330_G346_A0.5140.47
53_L365_D0.5130.47
167_Q177_T0.5130.47
159_I167_Q0.5130.47
212_R219_E0.5120.46
81_N328_S0.5120.46
351_V355_L0.5120.46
58_D242_T0.5100.46
80_M128_E0.5090.46
140_T150_T0.5090.46
168_E174_D0.5080.46
29_A33_E0.5080.46
96_G110_P0.5060.46
100_L103_L0.5050.46
241_E280_H0.5050.46
104_V110_P0.5050.46
49_E67_S0.5020.45
186_T200_T0.5010.45
350_T368_G0.5010.45
85_Y303_Q0.5010.45
28_L39_S0.5000.45
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  
1twfA 1 0.9521 100 0.149 Contact Map
3h0gA 2 0.9849 100 0.159 Contact Map
4c2mA 1 0.9496 100 0.16 Contact Map
4aybC 1 0.927 100 0.199 Contact Map
4qiwC 1 0.9194 100 0.203 Contact Map
4yfkD 1 0.6222 100 0.249 Contact Map
2a6hD 1 0.7028 100 0.355 Contact Map
1hqmD 1 0.7103 100 0.356 Contact Map
4iqzA 4 0.3073 99.8 0.831 Contact Map
3ltiA 1 0.2947 55.5 0.966 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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