GREMLIN Database
RPOA2 - DNA-directed RNA polymerase subunit A''
UniProt: P58192 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 392 (352)
Sequences: 2399 (1380)
Seq/√Len: 73.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
107_I290_I4.3881.00
96_N99_L3.7681.00
206_N209_N3.4901.00
277_I289_I3.3291.00
188_L191_G3.0451.00
39_I48_I3.0101.00
116_T128_K3.0091.00
197_E201_S2.9651.00
120_T123_L2.9261.00
285_A288_E2.8941.00
105_I145_K2.8661.00
295_S299_A2.8601.00
108_V138_A2.6941.00
100_G103_R2.5831.00
205_I208_A2.5771.00
292_R296_K2.4411.00
265_D268_K2.3891.00
142_E148_N2.3751.00
106_E110_A2.3741.00
288_E292_R2.2991.00
365_G368_E2.2811.00
194_M202_T2.2401.00
51_L60_L2.2241.00
124_T129_R2.2181.00
102_P106_E2.1251.00
46_D364_K2.0951.00
196_E202_T2.0581.00
197_E200_D2.0441.00
187_R190_L2.0051.00
204_N207_F1.9851.00
204_N208_A1.9451.00
165_Q171_L1.9101.00
353_D357_R1.9051.00
204_N209_N1.8841.00
117_P120_T1.8811.00
61_I65_E1.8701.00
117_P121_I1.8121.00
295_S305_V1.8041.00
342_A347_T1.7831.00
282_G285_A1.7531.00
161_S165_Q1.7191.00
195_I200_D1.7021.00
121_I125_D1.6941.00
107_I143_Y1.6901.00
313_I349_K1.6861.00
139_R142_E1.6771.00
347_T354_A1.6751.00
165_Q169_E1.6661.00
114_P117_P1.6561.00
145_K148_N1.6531.00
160_M166_L1.6431.00
201_S205_I1.6411.00
161_S171_L1.6361.00
369_N374_H1.6311.00
343_A347_T1.6140.99
193_F196_E1.6130.99
156_D196_E1.6070.99
92_I95_L1.5870.99
193_F205_I1.5870.99
117_P123_L1.5710.99
203_L208_A1.5630.99
203_L206_N1.5530.99
138_A148_N1.5440.99
83_T86_T1.5440.99
169_E173_D1.5220.99
168_N172_K1.5220.99
193_F197_E1.5030.99
115_S119_M1.4980.99
331_V340_A1.4910.99
165_Q173_D1.4850.99
169_E172_K1.4830.99
270_E292_R1.4780.99
49_F52_A1.4730.99
166_L171_L1.4670.99
316_V340_A1.4630.99
97_V102_P1.4560.99
120_T126_E1.4540.99
341_R359_D1.4490.99
49_F54_K1.4310.99
281_F285_A1.4310.99
188_L192_D1.4250.99
99_L102_P1.4160.99
196_E205_I1.4110.99
198_S201_S1.4050.99
241_K244_D1.4010.99
177_T180_D1.3930.98
75_V79_G1.3930.98
203_L207_F1.3870.98
129_R132_D1.3830.98
339_L370_I1.3680.98
202_T205_I1.3650.98
240_Q247_I1.3650.98
120_T124_T1.3550.98
195_I198_S1.3550.98
158_A194_M1.3450.98
197_E207_F1.3440.98
369_N377_K1.3300.98
135_L152_S1.3280.98
97_V100_G1.3170.98
116_T119_M1.3150.98
162_I166_L1.3130.98
100_G110_A1.3020.98
42_R49_F1.2960.98
298_L303_L1.2910.97
159_S163_I1.2910.97
158_A196_E1.2900.97
116_T120_T1.2860.97
202_T207_F1.2810.97
102_P110_A1.2750.97
100_G106_E1.2730.97
121_I124_T1.2680.97
252_G287_R1.2680.97
290_I294_I1.2590.97
161_S172_K1.2580.97
48_I186_G1.2520.97
180_D184_A1.2480.97
79_G326_I1.2400.97
125_D129_R1.2390.97
290_I314_A1.2360.97
169_E180_D1.2350.97
195_I202_T1.2310.97
42_R47_K1.2270.97
88_H91_G1.2220.96
98_T102_P1.2160.96
176_V185_I1.2030.96
103_R106_E1.2030.96
196_E201_S1.2020.96
51_L294_I1.2010.96
212_S215_A1.2000.96
254_N257_G1.1900.96
294_I319_R1.1880.96
117_P128_K1.1860.96
186_G190_L1.1860.96
61_I122_Y1.1790.96
171_L174_K1.1780.96
75_V267_A1.1670.95
84_L286_A1.1630.95
195_I199_E1.1540.95
68_G80_T1.1510.95
168_N171_L1.1500.95
133_K136_E1.1440.95
97_V284_E1.1370.95
36_K39_I1.1340.95
258_V264_V1.1320.95
101_L109_D1.1280.94
48_I52_A1.1270.94
167_D179_D1.1210.94
193_F201_S1.1190.94
202_T206_N1.1180.94
183_K186_G1.1080.94
327_G368_E1.1030.94
197_E202_T1.1010.94
42_R54_K1.0980.94
101_L106_E1.0950.93
176_V180_D1.0860.93
122_Y125_D1.0840.93
196_E207_F1.0800.93
137_V152_S1.0770.93
165_Q172_K1.0700.93
42_R46_D1.0690.93
175_G184_A1.0660.93
227_K232_K1.0650.93
109_D327_G1.0610.92
282_G286_A1.0590.92
201_S204_N1.0580.92
355_A365_G1.0550.92
201_S206_N1.0540.92
290_I321_G1.0510.92
160_M171_L1.0420.92
96_N100_G1.0420.92
201_S208_A1.0410.92
211_D214_A1.0370.91
295_S307_I1.0360.91
71_A313_I1.0340.91
272_N284_E1.0310.91
37_E42_R1.0220.91
202_T208_A1.0190.91
229_K241_K1.0170.91
158_A178_V1.0090.90
194_M205_I1.0060.90
363_F372_I1.0050.90
194_M207_F0.9980.90
68_G81_Q0.9970.90
284_E293_E0.9960.90
98_T104_L0.9920.90
117_P126_E0.9910.90
162_I165_Q0.9860.89
102_P111_K0.9840.89
205_I209_N0.9830.89
230_G342_A0.9810.89
160_M165_Q0.9800.89
245_E268_K0.9800.89
186_G192_D0.9770.89
298_L301_Q0.9740.89
99_L117_P0.9730.89
238_I251_D0.9730.89
167_D173_D0.9670.88
292_R323_V0.9640.88
371_I376_I0.9610.88
100_G284_E0.9570.88
119_M125_D0.9560.88
259_L269_V0.9540.88
89_F92_I0.9520.88
75_V313_I0.9510.88
101_L111_K0.9480.87
255_L259_L0.9440.87
49_F53_I0.9420.87
307_I311_L0.9410.87
163_I174_K0.9370.87
123_L126_E0.9310.86
197_E205_I0.9230.86
100_G107_I0.9230.86
103_R116_T0.9210.86
340_A370_I0.9190.86
164_L170_M0.9170.86
67_I312_L0.9170.86
107_I370_I0.9140.85
194_M198_S0.9120.85
141_L231_I0.9120.85
216_L223_I0.9090.85
200_D205_I0.9070.85
174_K185_I0.9050.85
69_I313_I0.9030.85
320_T324_R0.9020.85
123_L127_Y0.9010.85
327_G377_K0.9010.85
79_G85_R0.8990.84
210_I213_I0.8940.84
256_S261_V0.8920.84
103_R293_E0.8890.84
189_K192_D0.8870.84
180_D371_I0.8850.83
138_A142_E0.8820.83
59_G62_A0.8800.83
124_T263_G0.8790.83
56_Y287_R0.8750.83
117_P272_N0.8740.83
98_T103_R0.8700.82
31_N271_T0.8640.82
295_S310_I0.8630.82
319_R336_N0.8630.82
64_G361_E0.8620.82
51_L55_E0.8620.82
200_D208_A0.8610.82
222_K372_I0.8590.82
160_M173_D0.8590.82
31_N43_D0.8570.81
201_S207_F0.8550.81
294_I382_M0.8550.81
78_P88_H0.8550.81
187_R205_I0.8510.81
323_V327_G0.8480.81
96_N137_V0.8400.80
278_E323_V0.8380.80
281_F284_E0.8350.80
165_Q168_N0.8330.80
174_K177_T0.8320.80
89_F95_L0.8310.79
196_E203_L0.8310.79
317_M326_I0.8300.79
166_L181_V0.8300.79
193_F203_L0.8300.79
162_I171_L0.8300.79
270_E289_I0.8280.79
195_I203_L0.8270.79
226_T239_V0.8260.79
123_L134_A0.8220.79
170_M177_T0.8170.78
85_R298_L0.8160.78
62_A69_I0.8160.78
122_Y269_V0.8160.78
342_A350_H0.8150.78
252_G284_E0.8130.78
284_E321_G0.8070.77
325_Q377_K0.8070.77
194_M199_E0.8060.77
347_T371_I0.8040.77
184_A187_R0.8030.77
111_K331_V0.8020.77
347_T381_G0.8020.77
161_S167_D0.8010.77
227_K230_G0.8000.77
164_L174_K0.7970.77
79_G368_E0.7960.76
235_K296_K0.7960.76
274_I286_A0.7920.76
165_Q200_D0.7920.76
291_I314_A0.7900.76
42_R53_I0.7890.76
118_M128_K0.7880.76
48_I96_N0.7850.75
133_K155_I0.7840.75
324_R327_G0.7840.75
98_T110_A0.7820.75
110_A117_P0.7820.75
102_P107_I0.7810.75
101_L107_I0.7790.75
201_S209_N0.7770.75
68_G77_E0.7770.75
373_G379_G0.7760.75
166_L177_T0.7750.74
351_L368_E0.7750.74
126_E130_D0.7740.74
103_R149_V0.7740.74
168_N179_D0.7730.74
108_V294_I0.7720.74
340_A367_V0.7670.74
65_E301_Q0.7640.73
284_E385_L0.7610.73
107_I117_P0.7600.73
358_G362_E0.7590.73
290_I317_M0.7550.73
98_T106_E0.7540.72
105_I109_D0.7520.72
298_L350_H0.7470.72
104_L109_D0.7470.72
75_V307_I0.7460.72
346_V366_V0.7460.72
96_N223_I0.7450.72
136_E140_K0.7450.72
149_V228_I0.7450.72
108_V150_V0.7430.71
178_V181_V0.7410.71
171_L180_D0.7410.71
128_K131_R0.7390.71
99_L104_L0.7380.71
196_E200_D0.7340.70
200_D204_N0.7330.70
346_V349_K0.7310.70
320_T365_G0.7310.70
165_Q174_K0.7300.70
84_L328_R0.7280.70
325_Q351_L0.7260.70
103_R117_P0.7210.69
122_Y132_D0.7190.69
94_E271_T0.7190.69
326_I368_E0.7180.69
107_I110_A0.7160.69
100_G116_T0.7160.69
172_K183_K0.7160.69
93_R99_L0.7140.68
103_R285_A0.7110.68
163_I172_K0.7100.68
78_P82_M0.7090.68
100_G104_L0.7090.68
85_R341_R0.7070.68
347_T365_G0.7070.68
46_D312_L0.7070.68
160_M163_I0.7010.67
271_T321_G0.7000.67
47_K50_D0.6990.67
117_P122_Y0.6980.67
196_E204_N0.6970.66
117_P130_D0.6960.66
102_P284_E0.6950.66
162_I172_K0.6950.66
76_G81_Q0.6930.66
122_Y268_K0.6920.66
89_F300_E0.6910.66
102_P117_P0.6900.66
190_L196_E0.6900.66
99_L158_A0.6860.65
163_I171_L0.6850.65
193_F200_D0.6850.65
104_L290_I0.6840.65
40_V321_G0.6830.65
327_G343_A0.6820.65
122_Y247_I0.6820.65
102_P116_T0.6800.65
39_I262_K0.6790.64
85_R376_I0.6750.64
199_E202_T0.6730.64
329_H340_A0.6730.64
194_M201_S0.6710.64
142_E371_I0.6690.63
124_T131_R0.6680.63
186_G191_G0.6680.63
79_G301_Q0.6660.63
95_L98_T0.6620.62
186_G189_K0.6620.62
126_E129_R0.6610.62
180_D185_I0.6570.62
323_V368_E0.6560.62
42_R52_A0.6550.62
85_R325_Q0.6520.61
100_G293_E0.6520.61
124_T132_D0.6500.61
55_E58_E0.6490.61
82_M89_F0.6480.61
307_I329_H0.6470.61
197_E208_A0.6470.61
102_P149_V0.6460.61
194_M204_N0.6440.60
168_N205_I0.6440.60
110_A323_V0.6430.60
87_F91_G0.6420.60
136_E142_E0.6400.60
68_G76_G0.6400.60
38_I42_R0.6380.60
252_G255_L0.6380.60
164_L178_V0.6330.59
47_K54_K0.6330.59
248_I252_G0.6310.59
131_R241_K0.6300.59
277_I285_A0.6290.59
123_L130_D0.6280.58
96_N103_R0.6270.58
175_G181_V0.6230.58
132_D245_E0.6200.57
77_E80_T0.6170.57
320_T332_T0.6160.57
51_L54_K0.6150.57
107_I111_K0.6150.57
71_A316_V0.6140.57
67_I367_V0.6140.57
161_S166_L0.6130.57
117_P129_R0.6120.56
104_L107_I0.6120.56
286_A323_V0.6110.56
120_T318_T0.6100.56
255_L321_G0.6100.56
61_I341_R0.6080.56
76_G79_G0.6080.56
97_V103_R0.6070.56
301_Q367_V0.6050.56
100_G117_P0.6050.56
326_I347_T0.6040.56
296_K300_E0.6040.56
177_T199_E0.6030.55
338_V358_G0.6000.55
121_I258_V0.5990.55
63_P284_E0.5990.55
196_E209_N0.5980.55
182_K185_I0.5930.54
164_L169_E0.5930.54
63_P96_N0.5920.54
116_T139_R0.5920.54
176_V184_A0.5920.54
59_G67_I0.5910.54
325_Q342_A0.5900.54
57_S374_H0.5890.54
182_K186_G0.5880.54
157_I211_D0.5870.53
70_V270_E0.5870.53
210_I214_A0.5860.53
164_L185_I0.5780.52
183_K190_L0.5770.52
347_T351_L0.5770.52
178_V206_N0.5750.52
236_R240_Q0.5750.52
320_T355_A0.5750.52
64_G68_G0.5740.52
284_E287_R0.5740.52
61_I70_V0.5730.52
105_I146_I0.5700.51
83_T91_G0.5700.51
318_T323_V0.5700.51
163_I175_G0.5700.51
342_A352_L0.5690.51
40_V262_K0.5680.51
63_P383_V0.5670.51
172_K180_D0.5670.51
303_L310_I0.5660.51
283_I312_L0.5630.50
85_R301_Q0.5630.50
338_V350_H0.5620.50
89_F301_Q0.5610.50
121_I129_R0.5600.50
347_T350_H0.5600.50
297_V329_H0.5590.50
118_M127_Y0.5580.50
273_N284_E0.5560.50
301_Q340_A0.5560.50
166_L198_S0.5560.50
129_R271_T0.5560.50
93_R301_Q0.5550.49
226_T231_I0.5540.49
183_K193_F0.5520.49
71_A340_A0.5520.49
297_V354_A0.5500.49
103_R109_D0.5500.49
316_V338_V0.5490.49
166_L179_D0.5490.49
92_I101_L0.5480.49
78_P87_F0.5470.48
53_I377_K0.5450.48
191_G377_K0.5450.48
38_I53_I0.5400.48
164_L168_N0.5390.47
158_A169_E0.5390.47
71_A309_H0.5390.47
200_D211_D0.5380.47
324_R355_A0.5380.47
76_G80_T0.5370.47
264_V293_E0.5350.47
105_I111_K0.5350.47
195_I208_A0.5340.47
275_R278_E0.5340.47
104_L284_E0.5310.46
63_P102_P0.5310.46
219_L256_S0.5290.46
166_L169_E0.5280.46
73_Q81_Q0.5250.46
346_V350_H0.5250.46
47_K53_I0.5230.45
105_I117_P0.5230.45
250_T328_R0.5220.45
322_I359_D0.5200.45
53_I302_G0.5190.45
169_E176_V0.5190.45
104_L312_L0.5180.45
320_T327_G0.5170.45
225_N242_K0.5160.45
320_T333_G0.5130.44
172_K175_G0.5130.44
69_I290_I0.5120.44
73_Q76_G0.5120.44
57_S362_E0.5120.44
189_K195_I0.5110.44
298_L366_V0.5110.44
158_A198_S0.5090.44
108_V327_G0.5090.44
197_E206_N0.5080.44
100_G321_G0.5070.44
236_R248_I0.5050.43
298_L346_V0.5040.43
119_M128_K0.5040.43
112_K349_K0.5000.43
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  
4c2mA 1 0.949 100 0.162 Contact Map
1twfA 1 0.9668 100 0.169 Contact Map
3h0gA 2 0.9949 100 0.171 Contact Map
4aybC 1 0.9464 100 0.175 Contact Map
4qiwC 1 0.9413 100 0.186 Contact Map
4yfkD 1 0.625 100 0.256 Contact Map
2a6hD 1 0.7092 100 0.358 Contact Map
1hqmD 1 0.7194 100 0.366 Contact Map
4iqzA 4 0.3138 99.8 0.83 Contact Map
3ltiA 1 0.301 83.2 0.959 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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