LIPA - ECOLI - GREMLIN Contacts

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LIPA - Lipoyl synthase

UniProt:	P60716	Sequences: MSKPIVMERGVKYRDADKMALIPVKNVATEREALLRKPEWMKIKLPADSTRIQGIKAAMRKNGLHSVCEEASCPNLAECFNHGTATFMILGAICTRRCPFCDVAHGRPVAPDANEPVKLAQTIADMALRYVVITSVDRDDLRDGGAQHFADCITAIREKSPQIKIETLVPDFRGRMDRALDILTATPPDVFNHNLENVPRIYRQVRPGADYNWSLKLLERFKEAHPEIPTKSGLMVGLGETNEEIIEVMRDLRRHGVTMLTLGQYLQPSRHHLPVQRYVSPDEFDEMKAEALAMGFTHAACGPFVRSSYHADLQAKGMEVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11306
Length:	321 (283)
Sequences:	2193 (922)
Seq/√Len:	54.8

ECOLI - LIPA
BACSU - LIPA
HALSA - LIPA
SULSO - LIPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
90_L	111_P	5.260	1.00
249_M	260_L	4.221	1.00
169_V	191_F	3.728	1.00
200_R	244_E	3.708	1.00
250_R	294_M	3.605	1.00
277_R	283_E	3.545	1.00
211_Y	251_D	3.520	1.00
222_K	258_T	3.340	1.00
288_K	292_L	3.324	1.00
236_V	262_L	3.217	1.00
285_D	288_K	3.187	1.00
199_P	212_N	3.050	1.00
130_Y	164_K	2.998	1.00
242_N	286_E	2.742	1.00
155_A	158_E	2.617	1.00
246_I	290_E	2.598	1.00
119_L	152_C	2.560	1.00
232_S	252_L	2.474	1.00
89_I	133_I	2.298	1.00
114_N	117_V	2.278	1.00
160_S	163_I	2.250	1.00
302_G	305_V	2.248	1.00
153_I	167_T	2.206	1.00
242_N	283_E	2.203	1.00
147_Q	151_D	2.194	1.00
135_S	170_P	2.171	1.00
249_M	291_A	2.156	1.00
205_V	273_L	2.117	1.00
124_A	159_K	2.108	1.00
60_R	69_E	2.097	1.00
216_K	219_E	2.059	1.00
290_E	293_A	2.028	1.00
252_L	257_V	2.023	1.00
130_Y	190_V	2.012	1.00
242_N	287_M	1.952	1.00
144_G	179_A	1.942	1.00
181_D	224_A	1.937	1.00
100_F	209_A	1.896	1.00
92_A	104_A	1.879	0.99
72_S	102_D	1.853	0.99
279_V	287_M	1.824	0.99
117_V	155_A	1.822	0.99
191_F	221_F	1.803	0.99
199_P	202_Y	1.801	0.99
199_P	247_E	1.796	0.99
181_D	185_A	1.786	0.99
153_I	186_T	1.773	0.99
219_E	223_E	1.771	0.99
67_V	71_A	1.763	0.99
218_L	257_V	1.741	0.99
290_E	294_M	1.737	0.99
133_I	156_I	1.710	0.99
172_F	183_L	1.684	0.99
184_T	221_F	1.662	0.99
78_E	309_Y	1.647	0.99
291_A	299_A	1.643	0.99
157_R	165_I	1.622	0.98
51_R	54_G	1.618	0.98
199_P	248_V	1.601	0.98
117_V	121_Q	1.583	0.98
253_R	296_F	1.566	0.98
118_K	121_Q	1.544	0.98
88_M	103_V	1.534	0.98
150_A	154_T	1.503	0.97
283_E	287_M	1.502	0.97
220_R	223_E	1.495	0.97
286_E	290_E	1.493	0.97
82_H	312_D	1.470	0.97
52_I	76_L	1.445	0.97
175_R	179_A	1.426	0.96
212_N	216_K	1.408	0.96
58_A	125_D	1.382	0.96
43_I	304_F	1.378	0.96
155_A	159_K	1.376	0.96
151_D	154_T	1.372	0.96
62_N	122_T	1.362	0.95
236_V	287_M	1.353	0.95
61_K	125_D	1.345	0.95
156_I	163_I	1.338	0.95
181_D	220_R	1.336	0.95
90_L	148_H	1.330	0.95
253_R	294_M	1.325	0.95
146_A	182_I	1.306	0.94
112_D	118_K	1.279	0.94
99_P	273_L	1.273	0.93
289_A	293_A	1.264	0.93
253_R	256_G	1.260	0.93
184_T	225_H	1.252	0.93
62_N	125_D	1.246	0.93
123_I	160_S	1.239	0.92
93_I	106_G	1.235	0.92
216_K	220_R	1.233	0.92
202_Y	207_P	1.232	0.92
282_D	285_D	1.231	0.92
187_P	225_H	1.223	0.92
43_I	77_A	1.220	0.92
95_T	108_P	1.203	0.91
114_N	118_K	1.183	0.91
222_K	230_T	1.172	0.90
285_D	289_A	1.155	0.90
235_M	238_L	1.154	0.90
246_I	294_M	1.135	0.89
176_M	220_R	1.125	0.88
234_L	248_V	1.123	0.88
202_Y	210_D	1.116	0.88
252_L	260_L	1.114	0.88
70_E	92_A	1.113	0.88
117_V	159_K	1.103	0.87
35_L	278_Y	1.090	0.87
121_Q	125_D	1.087	0.87
63_G	118_K	1.086	0.86
137_D	213_W	1.082	0.86
236_V	245_I	1.073	0.86
124_A	160_S	1.052	0.85
220_R	224_A	1.046	0.84
221_F	228_I	1.046	0.84
121_Q	159_K	1.044	0.84
245_I	279_V	1.040	0.84
193_H	214_S	1.037	0.84
279_V	283_E	1.023	0.83
269_S	272_H	1.020	0.83
246_I	250_R	1.020	0.83
180_L	220_R	1.019	0.83
184_T	224_A	1.019	0.83
176_M	216_K	1.017	0.83
135_S	149_F	1.012	0.82
93_I	104_A	1.011	0.82
80_F	105_H	1.011	0.82
157_R	188_P	1.006	0.82
89_I	152_C	1.006	0.82
242_N	246_I	1.005	0.82
192_N	233_G	1.003	0.82
204_Q	276_Q	1.003	0.82
93_I	109_V	1.001	0.82
250_R	254_R	0.993	0.81
245_I	277_R	0.993	0.81
288_K	301_C	0.984	0.80
177_D	181_D	0.984	0.80
247_E	251_D	0.972	0.80
100_F	202_Y	0.964	0.79
56_K	69_E	0.956	0.79
184_T	191_F	0.952	0.78
37_K	72_S	0.950	0.78
206_R	209_A	0.950	0.78
128_L	131_V	0.948	0.78
184_T	228_I	0.948	0.78
151_D	155_A	0.944	0.78
65_H	92_A	0.939	0.77
183_L	187_P	0.938	0.77
283_E	286_E	0.933	0.77
52_I	80_F	0.932	0.77
54_G	83_G	0.926	0.76
156_I	160_S	0.917	0.76
150_A	183_L	0.912	0.75
267_Q	278_Y	0.900	0.74
87_F	119_L	0.895	0.74
300_A	310_H	0.893	0.74
147_Q	182_I	0.890	0.73
167_T	192_N	0.890	0.73
102_D	269_S	0.887	0.73
250_R	290_E	0.878	0.72
258_T	297_T	0.877	0.72
83_G	126_M	0.876	0.72
167_T	188_P	0.871	0.72
39_E	43_I	0.871	0.72
202_Y	208_G	0.863	0.71
249_M	290_E	0.856	0.70
55_I	126_M	0.848	0.70
232_S	262_L	0.847	0.70
174_G	213_W	0.843	0.69
123_I	131_V	0.842	0.69
123_I	163_I	0.842	0.69
176_M	180_L	0.839	0.69
207_P	233_G	0.835	0.69
152_C	156_I	0.833	0.68
202_Y	209_A	0.832	0.68
34_L	37_K	0.830	0.68
219_E	255_H	0.830	0.68
120_A	159_K	0.829	0.68
111_P	148_H	0.826	0.68
105_H	137_D	0.821	0.67
83_G	127_A	0.821	0.67
55_I	81_N	0.816	0.67
46_P	77_A	0.815	0.67
246_I	286_E	0.812	0.66
169_V	183_L	0.811	0.66
70_E	102_D	0.805	0.66
86_T	311_A	0.804	0.66
131_V	163_I	0.803	0.65
117_V	158_E	0.800	0.65
253_R	258_T	0.799	0.65
154_T	185_A	0.797	0.65
137_D	202_Y	0.797	0.65
113_A	148_H	0.796	0.65
40_W	281_P	0.790	0.64
170_P	183_L	0.787	0.64
36_R	39_E	0.787	0.64
58_A	62_N	0.772	0.62
76_L	80_F	0.769	0.62
249_M	253_R	0.768	0.62
137_D	172_F	0.767	0.62
195_L	248_V	0.767	0.62
221_F	225_H	0.766	0.62
243_E	246_I	0.764	0.62
150_A	182_I	0.762	0.61
88_M	300_A	0.761	0.61
123_I	156_I	0.761	0.61
219_E	256_G	0.759	0.61
252_L	255_H	0.751	0.60
280_S	283_E	0.747	0.60
45_L	77_A	0.745	0.60
230_T	258_T	0.743	0.59
102_D	137_D	0.741	0.59
169_V	172_F	0.735	0.59
199_P	203_R	0.735	0.59
164_K	189_D	0.733	0.58
59_M	80_F	0.732	0.58
144_G	173_R	0.732	0.58
249_M	294_M	0.731	0.58
273_L	276_Q	0.726	0.58
183_L	221_F	0.722	0.57
65_H	109_V	0.722	0.57
234_L	245_I	0.721	0.57
50_T	53_Q	0.719	0.57
169_V	221_F	0.718	0.57
298_H	310_H	0.716	0.57
180_L	217_L	0.716	0.57
215_L	255_H	0.714	0.56
280_S	285_D	0.713	0.56
153_I	165_I	0.713	0.56
292_L	299_A	0.710	0.56
173_R	179_A	0.710	0.56
242_N	279_V	0.710	0.56
238_L	273_L	0.709	0.56
154_T	186_T	0.709	0.56
247_E	250_R	0.708	0.56
202_Y	248_V	0.708	0.56
157_R	191_F	0.708	0.56
173_R	208_G	0.707	0.56
51_R	83_G	0.702	0.55
288_K	291_A	0.697	0.55
229_P	259_M	0.692	0.54
202_Y	212_N	0.688	0.54
167_T	191_F	0.688	0.54
129_R	312_D	0.685	0.53
300_A	314_Q	0.685	0.53
202_Y	233_G	0.685	0.53
191_F	217_L	0.683	0.53
135_S	172_F	0.682	0.53
261_T	305_V	0.681	0.53
57_A	61_K	0.681	0.53
37_K	266_L	0.680	0.53
249_M	296_F	0.679	0.53
180_L	191_F	0.679	0.53
259_M	314_Q	0.678	0.53
241_T	276_Q	0.676	0.52
250_R	293_A	0.674	0.52
246_I	293_A	0.671	0.52
80_F	202_Y	0.671	0.52
195_L	214_S	0.668	0.51
215_L	251_D	0.666	0.51
219_E	254_R	0.666	0.51
50_T	54_G	0.666	0.51
277_R	287_M	0.666	0.51
60_R	70_E	0.665	0.51
286_E	289_A	0.664	0.51
45_L	72_S	0.661	0.51
133_I	167_T	0.659	0.51
97_R	208_G	0.659	0.51
69_E	76_L	0.658	0.50
120_A	156_I	0.658	0.50
41_M	304_F	0.657	0.50
151_D	156_I	0.657	0.50
241_T	244_E	0.656	0.50
44_K	47_A	0.654	0.50
192_N	310_H	0.653	0.50
176_M	181_D	0.653	0.50
209_A	235_M	0.652	0.50
87_F	131_V	0.651	0.50
211_Y	247_E	0.650	0.50
39_E	282_D	0.648	0.49
291_A	300_A	0.647	0.49
232_S	255_H	0.647	0.49
183_L	186_T	0.646	0.49
184_T	222_K	0.646	0.49
148_H	300_A	0.644	0.49
65_H	69_E	0.642	0.49
97_R	105_H	0.641	0.49
236_V	279_V	0.640	0.48
121_Q	124_A	0.635	0.48
176_M	213_W	0.632	0.48
69_E	137_D	0.631	0.48
192_N	207_P	0.631	0.48
157_R	189_D	0.630	0.47
103_V	310_H	0.629	0.47
260_L	291_A	0.629	0.47
70_E	149_F	0.627	0.47
169_V	217_L	0.626	0.47
285_D	292_L	0.625	0.47
82_H	313_L	0.624	0.47
206_R	235_M	0.624	0.47
42_K	302_G	0.623	0.47
191_F	230_T	0.619	0.46
88_M	137_D	0.619	0.46
298_H	314_Q	0.618	0.46
97_R	137_D	0.613	0.46
180_L	224_A	0.613	0.46
167_T	186_T	0.611	0.45
197_N	236_V	0.611	0.45
48_D	52_I	0.611	0.45
245_I	262_L	0.608	0.45
207_P	210_D	0.607	0.45
280_S	301_C	0.606	0.45
51_R	81_N	0.605	0.45
33_A	270_R	0.604	0.45
149_F	192_N	0.604	0.45
167_T	233_G	0.601	0.44
145_G	170_P	0.600	0.44
132_V	263_G	0.598	0.44
110_A	148_H	0.597	0.44
195_L	232_S	0.596	0.44
80_F	210_D	0.596	0.44
137_D	257_V	0.593	0.43
262_L	287_M	0.593	0.43
253_R	260_L	0.591	0.43
272_H	307_S	0.590	0.43
52_I	55_I	0.589	0.43
99_P	102_D	0.587	0.43
187_P	221_F	0.586	0.43
87_F	126_M	0.584	0.43
197_N	205_V	0.582	0.42
266_L	278_Y	0.581	0.42
200_R	266_L	0.581	0.42
199_P	210_D	0.581	0.42
289_A	292_L	0.580	0.42
202_Y	217_L	0.579	0.42
200_R	247_E	0.579	0.42
217_L	220_R	0.577	0.42
102_D	105_H	0.576	0.42
110_A	113_A	0.571	0.41
221_F	229_P	0.571	0.41
233_G	310_H	0.570	0.41
62_N	118_K	0.569	0.41
284_F	301_C	0.568	0.41
122_T	125_D	0.567	0.41
67_V	207_P	0.566	0.41
181_D	291_A	0.566	0.41
195_L	211_Y	0.566	0.41
130_Y	165_I	0.560	0.40
238_L	276_Q	0.559	0.40
197_N	201_I	0.559	0.40
62_N	126_M	0.559	0.40
99_P	208_G	0.558	0.40
37_K	43_I	0.558	0.40
56_K	76_L	0.557	0.40
208_G	233_G	0.556	0.40
242_N	245_I	0.555	0.40
233_G	248_V	0.554	0.39
199_P	207_P	0.553	0.39
188_P	192_N	0.553	0.39
133_I	152_C	0.552	0.39
90_L	135_S	0.551	0.39
62_N	121_Q	0.551	0.39
259_M	300_A	0.550	0.39
312_D	315_A	0.549	0.39
43_I	76_L	0.548	0.39
291_A	314_Q	0.547	0.39
55_I	59_M	0.546	0.39
259_M	267_Q	0.545	0.39
43_I	46_P	0.544	0.38
52_I	257_V	0.544	0.38
167_T	172_F	0.544	0.38
42_K	287_M	0.540	0.38
244_E	247_E	0.538	0.38
88_M	133_I	0.536	0.38
102_D	126_M	0.535	0.37
58_A	118_K	0.535	0.37
124_A	250_R	0.534	0.37
100_F	195_L	0.534	0.37
119_L	131_V	0.533	0.37
72_S	97_R	0.531	0.37
51_R	55_I	0.530	0.37
281_P	303_P	0.530	0.37
88_M	148_H	0.529	0.37
192_N	261_T	0.529	0.37
157_R	187_P	0.527	0.37
183_L	225_H	0.525	0.36
162_Q	165_I	0.524	0.36
67_V	103_V	0.522	0.36
106_G	109_V	0.522	0.36
164_K	315_A	0.522	0.36
104_A	267_Q	0.522	0.36
44_K	51_R	0.521	0.36
245_I	287_M	0.521	0.36
245_I	249_M	0.520	0.36
129_R	156_I	0.519	0.36
37_K	44_K	0.518	0.36
310_H	314_Q	0.517	0.36
34_L	267_Q	0.517	0.36
37_K	169_V	0.516	0.36
67_V	88_M	0.516	0.36
205_V	235_M	0.516	0.36
140_D	208_G	0.515	0.36
288_K	300_A	0.514	0.35
298_H	315_A	0.514	0.35
212_N	247_E	0.512	0.35
235_M	307_S	0.512	0.35
243_E	253_R	0.512	0.35
169_V	180_L	0.512	0.35
93_I	107_R	0.510	0.35
197_N	209_A	0.510	0.35
157_R	192_N	0.510	0.35
243_E	282_D	0.509	0.35
182_I	187_P	0.509	0.35
117_V	151_D	0.507	0.35
129_R	158_E	0.506	0.35
135_S	202_Y	0.506	0.35
37_K	69_E	0.504	0.34
113_A	147_Q	0.502	0.34
99_P	202_Y	0.502	0.34
197_N	211_Y	0.501	0.34
267_Q	274_P	0.501	0.34
106_G	167_T	0.500	0.34
137_D	140_D	0.500	0.34

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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
4u0oB	1	0.8287	100	0.653	Contact Map
4r33A	2	0.8816	99.8	0.873	Contact Map
4wcxA	1	0.9159	99.7	0.879	Contact Map
3t7vA	1	0.8567	99.7	0.88	Contact Map
3iixA	1	0.8629	99.7	0.884	Contact Map
1r30A	2	0.8131	99.6	0.885	Contact Map
4rtbA	2	0.9097	99.6	0.886	Contact Map
2qgqA	1	0.6698	99.5	0.895	Contact Map
1oltA	1	0.8411	99.4	0.9	Contact Map
4jc0A	1	0.9595	99.4	0.902	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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