GREMLIN Database
RPOA - DNA-directed RNA polymerase subunit alpha
UniProt: P0A7Z4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10893
Length: 329 (302)
Sequences: 2098 (1096)
Seq/√Len: 63.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
56_V88_L5.6611.00
87_G128_H4.8351.00
205_M217_I4.5471.00
23_H206_E4.2621.00
109_P129_V3.7391.00
115_I144_I3.5991.00
25_K204_E3.5631.00
129_V132_H3.3881.00
89_A208_N3.3511.00
100_L146_V3.2941.00
105_S139_S3.2341.00
103_N141_S3.1921.00
57_T147_Q3.1821.00
104_K108_G3.0891.00
23_H204_E3.0381.00
62_D141_S3.0351.00
56_V85_L2.9951.00
147_Q177_Y2.9381.00
98_V118_D2.9231.00
59_V85_L2.8681.00
85_L88_L2.7741.00
74_V81_I2.6581.00
158_R175_A2.6021.00
60_E143_R2.5721.00
81_I130_I2.5611.00
91_R122_E2.5451.00
133_L138_A2.4041.00
99_I143_R2.3831.00
107_I136_E2.3731.00
188_E202_V2.3191.00
59_V82_L2.2281.00
125_K128_H2.1881.00
89_A210_T2.1531.00
90_V123_I2.1481.00
58_E145_K2.0841.00
263_T302_E2.0801.00
286_E304_K2.0651.00
93_Q122_E2.0601.00
104_K114_D2.0181.00
100_L144_I1.9961.00
42_A224_L1.9511.00
85_L144_I1.9501.00
88_L113_A1.9491.00
104_K133_L1.9211.00
224_L228_L1.9031.00
92_V121_V1.8961.00
295_L303_I1.8631.00
90_V146_V1.8581.00
64_V71_K1.8521.00
93_Q120_D1.8041.00
153_V177_Y1.7300.99
131_C140_I1.7290.99
28_L231_F1.6670.99
58_E170_R1.6610.99
109_P132_H1.6470.99
101_T143_R1.6420.99
101_T116_T1.5870.99
56_V144_I1.5830.99
192_V196_T1.5560.99
294_N299_S1.5470.99
255_R278_I1.5420.99
82_L171_L1.5380.99
296_G299_S1.5360.99
124_V210_T1.5230.99
79_L82_L1.5070.98
31_L39_L1.4670.98
88_L128_H1.4520.98
222_T226_E1.4460.98
103_N139_S1.4410.98
61_I78_I1.4390.98
92_V146_V1.4330.98
56_V173_V1.4260.98
88_L112_A1.4180.98
79_L171_L1.4100.98
278_I310_R1.4090.98
64_V78_I1.4050.98
225_A232_V1.3690.97
301_T305_D1.3560.97
28_L31_L1.3540.97
269_C294_N1.3490.97
46_I224_L1.3470.97
111_T129_V1.3100.96
150_R227_Q1.2940.96
303_I314_L1.2930.96
94_G120_D1.2830.96
57_T145_K1.2700.95
101_T141_S1.2570.95
59_V142_M1.2540.95
257_V267_A1.2320.95
182_R206_E1.2310.95
290_L295_L1.2210.94
89_A124_V1.2180.94
54_C148_R1.2180.94
289_L314_L1.2040.94
112_A126_P1.1960.94
133_L137_N1.1840.93
281_L307_L1.1760.93
203_I217_I1.1610.93
102_L110_V1.1580.93
265_R296_G1.1580.93
134_T137_N1.1450.92
307_L314_L1.1370.92
191_R199_D1.1280.92
268_N298_K1.1260.92
100_L121_V1.1120.91
265_R269_C1.1000.91
225_A228_L1.0900.90
191_R196_T1.0750.90
269_C299_S1.0700.89
44_R66_H1.0640.89
102_L140_I1.0550.89
266_S269_C1.0520.89
268_N296_G1.0490.88
110_V140_I1.0450.88
265_R268_N1.0360.88
31_L80_E1.0340.88
266_S294_N1.0310.88
173_V176_C1.0300.88
285_T315_G1.0290.87
184_A206_E1.0280.87
266_S299_S1.0280.87
54_C92_V1.0250.87
102_L142_M1.0240.87
308_A313_S1.0230.87
118_D121_V1.0220.87
108_G114_D1.0170.87
112_A125_K1.0160.87
36_G199_D1.0160.87
261_E269_C1.0120.87
285_T314_L1.0060.86
267_A271_K0.9970.86
29_E200_K0.9960.86
90_V210_T0.9890.85
219_R222_T0.9770.85
44_R67_E0.9740.84
97_E145_K0.9720.84
269_C295_L0.9680.84
51_M178_S0.9680.84
297_K301_T0.9600.84
71_K78_I0.9560.83
264_V294_N0.9530.83
215_E219_R0.9500.83
134_T138_A0.9460.83
292_T303_I0.9410.82
36_G187_V0.9400.82
102_L117_H0.9360.82
263_T289_L0.9280.81
275_I281_L0.9200.81
191_R197_D0.9190.81
57_T177_Y0.9140.80
52_P148_R0.9130.80
249_F254_L0.9070.80
292_T295_L0.9030.80
44_R68_Y0.9030.80
23_H26_V0.9030.80
258_D271_K0.9000.79
100_L115_I0.8980.79
188_E200_K0.8940.79
51_M90_V0.8900.79
150_R293_P0.8900.79
102_L115_I0.8850.78
252_I255_R0.8840.78
287_V317_R0.8830.78
108_G133_L0.8790.78
115_I142_M0.8760.78
253_L282_V0.8760.78
103_N116_T0.8750.77
262_L278_I0.8750.77
154_P175_A0.8690.77
211_I215_E0.8680.77
215_E218_R0.8610.76
298_K301_T0.8580.76
149_G153_V0.8570.76
20_S125_K0.8560.76
99_I145_K0.8450.75
262_L307_L0.8430.75
60_E141_S0.8400.74
24_A206_E0.8380.74
184_A204_E0.8380.74
189_A197_D0.8350.74
91_R215_E0.8310.74
284_R288_E0.8210.73
273_E289_L0.8190.73
232_V236_D0.8130.72
192_V198_L0.8120.72
267_A303_I0.8090.72
88_L144_I0.8080.72
251_P255_R0.8020.71
102_L130_I0.8000.71
64_V81_I0.7990.71
304_K308_A0.7960.70
55_A175_A0.7950.70
87_G181_E0.7910.70
124_V208_N0.7900.70
17_E25_K0.7870.70
191_R198_L0.7860.69
264_V268_N0.7820.69
227_Q277_Y0.7770.69
98_V120_D0.7760.69
191_R194_Q0.7720.68
110_V131_C0.7690.68
305_D308_A0.7660.68
272_A315_G0.7650.67
115_I130_I0.7640.67
82_L173_V0.7640.67
223_I227_Q0.7590.67
189_A196_T0.7550.66
204_E248_E0.7540.66
41_N45_R0.7520.66
100_L117_H0.7500.66
293_P306_V0.7490.66
52_P219_R0.7430.65
254_L277_Y0.7420.65
190_A199_D0.7420.65
32_E150_R0.7400.65
300_L312_L0.7390.65
201_L217_I0.7380.65
60_E167_P0.7360.64
93_Q119_G0.7350.64
31_L201_L0.7330.64
95_K98_V0.7310.64
244_E249_F0.7300.64
276_H280_D0.7300.64
185_Y188_E0.7300.64
252_I310_R0.7300.64
255_R261_E0.7260.63
54_C90_V0.7260.63
228_L232_V0.7240.63
40_G201_L0.7240.63
255_R310_R0.7210.63
282_V285_T0.7170.62
74_V131_C0.7160.62
74_V130_I0.7140.62
131_C134_T0.7090.62
304_K312_L0.7050.61
296_G302_E0.7050.61
267_A276_H0.7040.61
112_A216_A0.7020.61
144_I173_V0.7020.61
102_L183_I0.6990.60
221_A231_F0.6970.60
115_I118_D0.6950.60
274_A315_G0.6920.60
153_V158_R0.6890.59
97_E147_Q0.6860.59
193_E212_D0.6850.59
128_H145_K0.6830.59
162_E166_R0.6830.59
92_V100_L0.6790.58
37_H185_Y0.6780.58
265_R298_K0.6780.58
282_V315_G0.6760.58
272_A316_M0.6750.58
74_V78_I0.6730.58
90_V117_H0.6720.57
60_E209_G0.6720.57
93_Q118_D0.6710.57
71_K132_H0.6700.57
106_G109_P0.6700.57
265_R302_E0.6690.57
306_V310_R0.6690.57
29_E190_A0.6690.57
31_L62_D0.6680.57
226_E232_V0.6670.57
147_Q280_D0.6660.57
273_E299_S0.6660.57
112_A182_R0.6660.57
235_R257_V0.6630.56
271_K298_K0.6630.56
145_K170_R0.6630.56
88_L182_R0.6620.56
292_T306_V0.6620.56
63_G174_D0.6590.56
27_T200_K0.6560.56
211_I216_A0.6550.55
109_P128_H0.6550.55
64_V73_G0.6530.55
295_L299_S0.6520.55
222_T297_K0.6520.55
281_L303_I0.6490.55
284_R289_L0.6490.55
35_F50_S0.6490.55
163_E173_V0.6470.55
274_A280_D0.6460.54
277_Y281_L0.6410.54
295_L316_M0.6410.54
266_S298_K0.6390.54
269_C273_E0.6370.53
35_F245_E0.6360.53
26_V217_I0.6360.53
305_D309_S0.6350.53
226_E229_E0.6340.53
64_V69_S0.6330.53
62_D65_L0.6310.53
187_V190_A0.6300.53
115_I123_I0.6290.53
113_A127_Q0.6280.52
73_G137_N0.6280.52
272_A301_T0.6280.52
133_L142_M0.6270.52
272_A292_T0.6250.52
60_E170_R0.6230.52
31_L40_G0.6230.52
89_A125_K0.6210.52
147_Q208_N0.6180.51
73_G83_L0.6180.51
251_P254_L0.6170.51
292_T315_G0.6160.51
42_A300_L0.6130.51
253_L279_G0.6120.51
272_A295_L0.6100.50
264_V269_C0.6080.50
37_H199_D0.6080.50
25_K186_N0.6070.50
241_E246_K0.6070.50
236_D240_P0.6060.50
90_V144_I0.6050.50
39_L227_Q0.6040.50
268_N294_N0.6040.50
121_V146_V0.6040.50
251_P303_I0.6030.50
125_K202_V0.6010.49
267_A289_L0.6010.49
68_Y171_L0.6010.49
180_V207_T0.6010.49
66_H78_I0.6000.49
90_V100_L0.6000.49
285_T292_T0.5990.49
150_R178_S0.5970.49
192_V197_D0.5970.49
267_A290_L0.5950.49
35_F189_A0.5950.49
158_R162_E0.5940.48
287_V316_M0.5930.48
124_V128_H0.5920.48
35_F227_Q0.5920.48
32_E191_R0.5900.48
78_I81_I0.5900.48
65_L169_G0.5900.48
262_L266_S0.5890.48
31_L231_F0.5880.48
265_R299_S0.5850.47
85_L130_I0.5850.47
189_A195_R0.5850.47
51_M216_A0.5830.47
97_E131_C0.5820.47
222_T225_A0.5820.47
104_K110_V0.5790.47
131_C204_E0.5760.46
66_H70_T0.5760.46
41_N302_E0.5760.46
227_Q230_A0.5750.46
261_E306_V0.5720.46
74_V133_L0.5720.46
266_S306_V0.5710.46
294_N298_K0.5690.46
49_S74_V0.5690.46
144_I205_M0.5690.46
221_A225_A0.5680.45
90_V124_V0.5660.45
279_G282_V0.5660.45
162_E167_P0.5660.45
222_T232_V0.5650.45
177_Y216_A0.5650.45
273_E293_P0.5640.45
210_T281_L0.5610.45
243_K246_K0.5610.45
258_D274_A0.5610.45
262_L270_L0.5610.45
306_V309_S0.5600.45
241_E244_E0.5600.45
303_I315_G0.5600.45
194_Q197_D0.5590.44
74_V104_K0.5590.44
24_A273_E0.5580.44
123_I210_T0.5560.44
249_F278_I0.5560.44
64_V67_E0.5550.44
284_R290_L0.5550.44
112_A128_H0.5550.44
228_L267_A0.5540.44
27_T202_V0.5540.44
198_L214_E0.5530.44
26_V214_E0.5530.44
117_H126_P0.5510.44
286_E312_L0.5500.43
92_V173_V0.5470.43
111_T128_H0.5470.43
20_S35_F0.5450.43
57_T97_E0.5440.43
138_A230_A0.5440.43
61_I64_V0.5430.43
36_G40_G0.5430.43
31_L314_L0.5420.43
105_S141_S0.5410.42
262_L269_C0.5400.42
77_D168_I0.5400.42
101_T107_I0.5390.42
23_H184_A0.5390.42
264_V299_S0.5380.42
237_V242_V0.5380.42
80_E197_D0.5370.42
59_V79_L0.5360.42
91_R148_R0.5360.42
85_L140_I0.5360.42
45_R66_H0.5350.42
102_L116_T0.5350.42
282_V310_R0.5340.42
153_V175_A0.5330.42
279_G283_Q0.5330.42
80_E214_E0.5330.42
264_V298_K0.5300.41
158_R172_L0.5300.41
46_I220_A0.5300.41
56_V90_V0.5290.41
98_V257_V0.5290.41
64_V171_L0.5270.41
218_R292_T0.5260.41
28_L297_K0.5250.41
15_D309_S0.5250.41
102_L114_D0.5250.41
117_H120_D0.5240.41
125_K201_L0.5240.41
44_R47_L0.5240.41
86_K174_D0.5230.40
69_S184_A0.5230.40
46_I51_M0.5230.40
119_G137_N0.5230.40
91_R171_L0.5220.40
157_T195_R0.5210.40
163_E166_R0.5200.40
84_N130_I0.5190.40
213_P267_A0.5190.40
123_I214_E0.5180.40
261_E290_L0.5180.40
162_E245_E0.5180.40
298_K302_E0.5170.40
90_V208_N0.5150.40
243_K247_P0.5150.40
60_E169_G0.5150.40
252_I279_G0.5140.39
51_M211_I0.5120.39
227_Q293_P0.5120.39
297_K300_L0.5120.39
35_F224_L0.5120.39
232_V288_E0.5110.39
45_R68_Y0.5110.39
67_E150_R0.5090.39
291_K306_V0.5070.39
90_V128_H0.5050.38
43_L46_I0.5020.38
155_A283_Q0.5000.38
140_I311_G0.5000.38
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  
4yfkA 2 0.9726 100 0.16 Contact Map
4noiA 2 0.69 100 0.179 Contact Map
2a6hA 2 0.69 100 0.206 Contact Map
1bdfA 4 0.7052 100 0.401 Contact Map
2pa8D 1 0.6596 100 0.536 Contact Map
4qjvA 1 0.6596 100 0.544 Contact Map
4c2mC 1 0.693 100 0.555 Contact Map
1twfC 1 0.693 100 0.567 Contact Map
3h0gC 1 0.6748 100 0.574 Contact Map
2maxA 1 0.3131 99.9 0.79 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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