GREMLIN Database
RPOA - DNA-directed RNA polymerase subunit alpha
UniProt: P20429 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 314 (300)
Sequences: 2101 (1114)
Seq/√Len: 64.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
53_V85_L5.8921.00
84_K125_L4.7701.00
198_V210_I4.4701.00
20_F199_W4.2201.00
106_T126_H3.6001.00
112_I140_L3.5791.00
22_K197_D3.5521.00
97_L142_A3.4551.00
86_A201_D3.3461.00
126_H129_T3.3051.00
102_Q135_S3.1731.00
54_T143_Q3.1171.00
100_D137_R3.1101.00
20_F197_D3.0861.00
53_V82_I3.0221.00
59_D137_R3.0031.00
101_V105_G2.9701.00
56_I82_I2.9601.00
143_Q170_Y2.8571.00
95_K115_D2.7811.00
82_I85_L2.7261.00
71_V78_I2.7181.00
57_Q139_R2.5251.00
88_K119_E2.5061.00
78_I127_I2.4941.00
130_L134_A2.4281.00
154_N168_S2.3151.00
96_T139_R2.3091.00
181_E195_T2.2901.00
282_E300_K2.1091.00
86_A203_S2.0941.00
56_I79_I2.0921.00
122_N125_L2.0771.00
87_L120_I2.0641.00
55_S141_T2.0521.00
85_L110_A2.0501.00
259_S298_E2.0461.00
101_V111_D2.0021.00
82_I140_L1.9761.00
97_L140_L1.9761.00
104_E132_E1.9641.00
61_V68_I1.9551.00
291_L299_V1.9411.00
90_Y119_E1.8991.00
39_S217_L1.8831.00
128_A136_F1.8681.00
101_V130_L1.8251.00
217_L221_L1.8191.00
87_L142_A1.7791.00
89_I118_V1.7681.00
25_V224_F1.7511.00
55_S163_V1.7481.00
149_T170_Y1.7200.99
274_V306_L1.6880.99
90_Y117_D1.6610.99
106_T129_T1.6490.99
98_E139_R1.6290.99
251_M274_V1.6190.99
185_V189_A1.5900.99
290_N295_S1.5900.99
121_L203_S1.5890.99
79_I164_I1.5590.99
85_L125_L1.5430.99
53_V140_L1.5370.99
61_V75_V1.5150.99
76_T79_I1.5120.99
292_G295_S1.5000.98
98_E113_T1.4920.98
76_T164_I1.4180.98
215_K219_E1.4150.98
265_C290_N1.4010.98
28_L36_L1.3830.97
100_D135_S1.3830.97
299_V310_L1.3820.97
58_I75_V1.3800.97
85_L109_A1.3750.97
25_V28_L1.3580.97
56_I138_V1.3440.97
303_L310_L1.3350.97
297_E301_A1.3340.97
91_S117_D1.3310.97
146_R220_H1.3210.97
43_I217_L1.2880.96
108_T126_H1.2810.96
253_I263_Y1.2760.96
53_V166_I1.2580.96
218_T225_V1.2360.95
286_M291_L1.2190.95
54_T141_T1.1970.94
175_R199_W1.1930.94
98_E137_R1.1930.94
86_A121_L1.1850.94
99_I136_F1.1840.94
184_R192_D1.1820.94
285_M310_L1.1630.93
51_A144_R1.1550.93
277_L303_L1.1450.93
261_R264_N1.1390.92
89_I142_A1.1350.92
99_I107_V1.1340.92
196_L210_I1.1320.92
97_L118_V1.1210.92
264_N294_K1.1210.92
130_L133_N1.1130.92
218_T221_L1.0940.91
265_C295_S1.0940.91
261_R292_G1.0890.91
109_A123_P1.0810.90
262_S265_C1.0770.90
177_S199_W1.0750.90
41_R63_H1.0730.90
288_V299_V1.0660.90
166_I169_I1.0640.90
261_R265_C1.0640.90
225_V229_D1.0610.89
184_R189_A1.0530.89
262_S295_S1.0490.89
262_S290_N1.0470.89
107_V136_F1.0430.89
257_D265_C1.0390.88
28_L77_T1.0370.88
87_L203_S1.0310.88
41_R64_E1.0270.88
293_R297_E1.0260.88
33_G180_V1.0200.88
264_N292_G1.0160.87
68_I75_V1.0130.87
115_D118_V1.0100.87
33_G192_D1.0100.87
51_A89_I1.0070.87
184_R190_N1.0060.87
109_A122_N1.0060.87
131_G134_A0.9980.86
99_I112_I0.9950.86
260_V290_N0.9890.86
48_L171_T0.9860.86
99_I138_V0.9810.85
249_L278_A0.9810.85
26_E193_K0.9790.85
150_P168_S0.9790.85
100_D113_T0.9770.85
99_I114_H0.9740.85
265_C291_L0.9690.85
146_R289_R0.9670.85
304_E309_G0.9630.84
281_T310_L0.9620.84
49_P144_R0.9600.84
245_K250_E0.9500.84
263_Y267_K0.9450.83
185_V191_Y0.9400.83
288_V291_L0.9360.83
97_L112_I0.9250.82
94_E141_T0.9240.82
254_E267_K0.9200.82
41_R65_F0.9110.81
57_Q137_R0.9100.81
271_I277_L0.9070.81
281_T311_R0.9030.80
105_G111_D0.9020.80
263_Y299_V0.8920.79
181_E193_K0.8910.79
259_S285_M0.8900.79
258_L303_L0.8850.79
208_E212_L0.8810.79
54_T170_Y0.8790.78
294_K297_E0.8750.78
268_R311_R0.8710.78
105_G130_L0.8710.78
280_K284_D0.8680.78
212_L215_K0.8650.77
182_N190_N0.8630.77
84_K174_S0.8620.77
20_F23_F0.8620.77
48_L87_L0.8610.77
17_D122_N0.8610.77
208_E211_A0.8580.77
112_I138_V0.8540.76
248_V251_M0.8530.76
220_H273_T0.8530.76
269_A285_M0.8380.75
99_I127_I0.8330.75
247_K251_M0.8260.74
184_R191_Y0.8250.74
38_N42_R0.8170.73
96_T141_T0.8130.73
75_V78_I0.8120.73
88_K208_E0.8120.73
95_K117_D0.8100.73
258_L274_V0.8070.72
90_Y116_S0.8060.72
228_T253_I0.8060.72
21_G199_W0.8060.72
289_R302_K0.8020.72
300_K304_E0.8010.72
177_S197_D0.7980.71
65_F164_I0.7930.71
71_V127_I0.7910.71
272_N276_E0.7910.71
260_V264_N0.7880.70
85_L140_L0.7860.70
130_L138_V0.7860.70
52_A168_S0.7830.70
182_N189_A0.7820.70
194_L210_I0.7730.69
97_L114_H0.7710.69
28_L59_D0.7670.68
183_T192_D0.7670.68
288_V302_K0.7660.68
112_I127_I0.7610.68
79_I166_I0.7610.68
68_I129_T0.7600.68
250_E273_T0.7580.67
216_I220_H0.7550.67
83_K167_D0.7540.67
178_Y181_E0.7520.67
85_L175_R0.7510.67
251_M306_L0.7510.67
61_V78_I0.7500.67
237_M240_K0.7500.67
263_Y272_N0.7460.66
145_G149_T0.7460.66
121_L201_D0.7430.66
268_R312_K0.7420.66
110_A124_D0.7390.66
292_G298_E0.7370.65
251_M257_D0.7370.65
278_A281_T0.7350.65
128_A131_G0.7310.65
99_I176_V0.7300.65
180_V183_T0.7290.64
221_L225_V0.7260.64
300_K308_L0.7260.64
185_V190_N0.7240.64
109_A209_A0.7240.64
37_G194_L0.7200.63
215_K293_R0.7190.63
268_R288_V0.7170.63
296_L308_L0.7170.63
32_Y47_S0.7140.63
204_T208_E0.7120.63
141_T163_V0.7070.62
261_R294_K0.7070.62
273_T277_L0.7010.61
61_V70_G0.6950.61
23_F210_I0.6930.61
278_A311_R0.6920.60
120_I203_S0.6910.60
51_A87_L0.6900.60
26_E183_T0.6900.60
219_E222_N0.6890.60
32_Y182_N0.6890.60
140_L166_I0.6880.60
94_E143_Q0.6850.60
278_A312_K0.6850.60
267_K294_K0.6830.59
288_V311_R0.6820.59
32_Y217_L0.6820.59
29_E146_R0.6810.59
71_V128_A0.6800.59
152_D155_K0.6800.59
260_V265_C0.6790.59
226_G229_D0.6780.59
136_F307_G0.6780.59
107_V128_A0.6770.59
57_Q160_P0.6700.58
173_V200_T0.6680.58
12_V16_D0.6680.58
33_G37_G0.6670.58
204_T209_A0.6660.57
59_D62_L0.6620.57
87_L114_H0.6610.57
24_V195_T0.6610.57
269_A295_S0.6600.57
261_R298_E0.6590.57
146_R171_T0.6590.57
248_V306_L0.6540.56
34_T192_D0.6530.56
265_C269_A0.6520.56
28_L194_L0.6510.56
57_Q163_V0.6510.56
280_K285_M0.6500.56
143_Q201_D0.6500.56
197_D244_Q0.6500.56
28_L224_F0.6490.56
125_L141_T0.6480.55
17_D32_Y0.6480.55
277_L299_V0.6450.55
49_P212_L0.6450.55
263_Y285_M0.6440.55
291_L295_S0.6430.55
215_K218_T0.6400.55
281_T288_V0.6390.54
270_G276_E0.6380.54
123_P170_Y0.6370.54
143_Q276_E0.6350.54
154_N165_P0.6330.54
283_E312_K0.6320.54
149_T168_S0.6320.54
264_N290_N0.6320.54
214_S224_F0.6320.54
122_N195_T0.6280.53
36_L220_H0.6270.53
258_L262_S0.6260.53
87_L125_L0.6250.53
74_D161_I0.6250.53
268_R297_E0.6230.53
262_S294_K0.6220.52
109_A175_R0.6220.52
54_T94_E0.6200.52
58_I61_V0.6190.52
89_I97_L0.6180.52
302_K305_E0.6170.52
28_L37_G0.6140.52
270_G311_R0.6130.51
261_R295_S0.6110.51
301_A304_E0.6080.51
186_G191_Y0.6070.51
106_T125_L0.6070.51
34_T178_Y0.6040.50
103_G106_T0.6040.50
268_R291_L0.6020.50
114_H117_D0.6020.50
291_L312_K0.6010.50
259_S291_L0.6010.50
38_N298_E0.6000.50
219_E227_L0.5990.50
252_T257_D0.5970.50
32_Y220_H0.5960.49
269_A289_R0.5930.49
86_A122_N0.5920.49
66_S210_I0.5910.49
124_D204_T0.5890.49
63_H67_T0.5880.48
203_S277_L0.5870.48
254_E270_G0.5840.48
130_L217_L0.5840.48
293_R296_L0.5840.48
90_Y115_D0.5820.48
46_S71_V0.5820.48
24_V193_K0.5790.47
61_V66_S0.5770.47
48_L208_E0.5760.47
57_Q202_G0.5750.47
280_K286_M0.5730.47
134_A223_I0.5730.47
112_I115_D0.5700.46
62_L162_G0.5700.46
87_L201_D0.5700.46
219_E225_V0.5680.46
99_I111_D0.5660.46
87_L121_L0.5650.46
50_G168_S0.5640.46
290_N294_K0.5620.45
60_G167_D0.5590.45
65_F74_D0.5580.45
53_V87_L0.5580.45
301_A305_E0.5580.45
258_L266_L0.5580.45
114_H123_P0.5580.45
112_I120_I0.5580.45
82_I97_L0.5550.45
260_V295_S0.5550.45
184_R187_Q0.5540.45
279_N288_V0.5530.44
186_G190_N0.5530.44
142_A230_E0.5530.44
248_V275_Q0.5520.44
156_R159_Q0.5510.44
140_L198_V0.5500.44
66_S177_S0.5500.44
61_V64_E0.5490.44
299_V311_R0.5470.44
42_R63_H0.5460.44
94_E139_R0.5460.44
249_L275_Q0.5460.44
63_H75_V0.5450.44
15_S69_E0.5440.43
215_K225_V0.5430.43
74_D216_I0.5420.43
257_D302_K0.5420.43
70_G133_N0.5400.43
294_K298_E0.5400.43
36_L194_L0.5400.43
282_E308_L0.5400.43
263_Y286_M0.5390.43
258_L265_C0.5390.43
84_K103_G0.5380.43
118_V142_A0.5380.43
219_E229_D0.5380.43
42_R65_F0.5380.43
247_K250_E0.5380.43
160_P163_V0.5380.43
22_K179_Q0.5370.43
94_E128_A0.5350.42
21_G173_V0.5330.42
77_T207_K0.5330.42
71_V130_L0.5310.42
31_G35_T0.5310.42
221_L263_Y0.5290.42
245_K272_N0.5290.42
87_L140_L0.5290.42
89_I166_I0.5280.42
48_L209_A0.5270.41
81_H127_I0.5270.41
245_K274_V0.5270.41
220_H223_I0.5270.41
121_L125_L0.5260.41
260_V294_K0.5260.41
302_K306_L0.5250.41
88_K144_R0.5240.41
43_I48_L0.5240.41
43_I213_G0.5240.41
87_L97_L0.5240.41
101_V107_V0.5230.41
92_D233_H0.5230.41
44_L178_Y0.5230.41
257_D286_M0.5230.41
57_Q162_G0.5230.41
263_Y269_A0.5220.41
262_S302_K0.5220.41
109_A125_L0.5200.41
246_E274_V0.5190.41
254_E294_K0.5180.40
23_F199_W0.5170.40
44_L217_L0.5160.40
235_E306_L0.5160.40
116_S133_N0.5160.40
236_I240_K0.5150.40
211_A288_V0.5150.40
70_G80_L0.5150.40
128_A166_I0.5150.40
136_F231_A0.5130.40
144_R201_D0.5130.40
79_I310_L0.5110.40
28_L310_L0.5110.40
198_V301_A0.5110.40
247_K299_V0.5110.40
275_Q278_A0.5100.40
40_L43_I0.5090.39
71_V75_V0.5090.39
206_P263_Y0.5080.39
71_V101_V0.5080.39
12_V15_S0.5070.39
78_I128_A0.5070.39
31_G184_R0.5070.39
155_K165_P0.5060.39
148_Y214_S0.5020.39
290_N298_E0.5010.39
226_G248_V0.5000.38
18_A135_S0.5000.38
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  
2a6hA 2 0.7229 100 0.173 Contact Map
4yfkA 2 0.9841 100 0.182 Contact Map
4noiA 2 0.7134 100 0.192 Contact Map
1bdfA 4 0.7197 100 0.407 Contact Map
2pa8D 1 0.6815 100 0.521 Contact Map
4qjvA 1 0.6815 100 0.528 Contact Map
4c2mC 1 0.7102 100 0.546 Contact Map
1twfC 1 0.7166 100 0.554 Contact Map
3h0gC 1 0.6975 100 0.561 Contact Map
2maxA 1 0.293 99.9 0.797 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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