LIPA - BACSU - GREMLIN Contacts

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LIPA - Lipoyl synthase

UniProt:	O32129	Sequences: MAKKDEHLRKPEWLKIKLNTNENYTGLKKLMRENNLHTVCEEAKCPNIHECWAVRRTATFMILGSVCTRACRFCAVKTGLPTELDLQEPERVADSVALMNLKHAVITAVARDDQKDGGAGIFAETVRAIRRKSPFTTIEVLPSDMGGNYDNLKTLMDTRPDILNHNIETVRRLTPRVRARATYDRSLEFLRRAKEMQPDIPTKSSIMIGLGETKEEIIEVMDDLLANNVDIMAIGQYLQPTKKHLKVQKYYHPDEFAELKEIAMQKGFSHCEAGPLVRSSYHADEQVNEASKKRQAQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	298 (281)
Sequences:	2204 (921)
Seq/√Len:	54.9

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
63_L	84_L	5.230	1.00
221_M	232_M	4.289	1.00
142_P	163_L	3.685	1.00
172_R	216_E	3.662	1.00
249_K	255_E	3.584	1.00
183_Y	223_D	3.536	1.00
222_D	266_K	3.473	1.00
260_K	264_M	3.349	1.00
194_K	230_D	3.284	1.00
208_I	234_I	3.274	1.00
257_A	260_K	3.226	1.00
171_R	184_D	2.965	1.00
103_H	137_T	2.908	1.00
214_K	258_E	2.706	1.00
218_I	262_I	2.558	1.00
128_A	131_R	2.544	1.00
92_V	125_T	2.524	1.00
204_S	224_L	2.386	1.00
62_I	106_I	2.357	1.00
274_G	277_V	2.245	1.00
126_V	140_V	2.244	1.00
120_G	124_E	2.240	1.00
87_Q	90_E	2.232	1.00
133_S	136_T	2.202	1.00
108_A	143_S	2.181	1.00
214_K	255_E	2.155	1.00
221_M	263_A	2.139	1.00
177_V	245_L	2.113	1.00
32_R	41_E	2.063	1.00
97_A	132_K	2.038	1.00
214_K	259_L	2.002	1.00
262_I	265_Q	1.975	1.00
224_L	229_V	1.953	1.00
117_G	151_N	1.946	1.00
188_E	191_R	1.937	1.00
103_H	162_I	1.930	1.00
73_F	181_A	1.913	1.00
153_K	196_M	1.895	1.00
90_E	128_A	1.864	0.99
39_V	43_A	1.822	0.99
65_S	77_K	1.816	0.99
44_K	75_A	1.813	0.99
251_Y	259_L	1.797	0.99
126_V	158_T	1.796	0.99
163_L	193_A	1.763	0.99
191_R	195_E	1.755	0.99
153_K	157_D	1.750	0.99
171_R	174_T	1.737	0.99
171_R	219_E	1.734	0.99
262_I	266_K	1.727	0.99
106_I	129_I	1.725	0.99
156_M	193_A	1.715	0.99
190_L	229_V	1.707	0.99
145_M	155_L	1.688	0.99
23_N	26_G	1.678	0.99
263_A	271_C	1.624	0.98
50_E	281_Y	1.596	0.98
171_R	220_V	1.594	0.98
130_R	138_I	1.561	0.98
55_R	284_D	1.554	0.98
91_R	94_D	1.542	0.98
61_M	76_V	1.533	0.98
225_L	268_F	1.528	0.98
24_Y	48_I	1.525	0.98
90_E	94_D	1.521	0.98
258_E	262_I	1.499	0.97
255_E	259_L	1.446	0.97
148_N	151_N	1.440	0.97
192_R	195_E	1.433	0.97
124_E	127_R	1.430	0.97
30_L	98_L	1.375	0.96
72_R	245_L	1.363	0.95
153_K	192_R	1.362	0.95
123_A	127_R	1.360	0.95
225_L	266_K	1.358	0.95
184_D	188_E	1.339	0.95
34_N	95_S	1.338	0.95
63_L	121_I	1.326	0.95
128_A	132_K	1.325	0.95
16_I	276_L	1.305	0.94
225_L	228_N	1.304	0.94
33_E	98_L	1.300	0.94
119_A	154_T	1.293	0.94
96_V	133_S	1.288	0.94
129_I	136_T	1.286	0.94
208_I	259_L	1.284	0.94
85_D	91_R	1.281	0.94
149_Y	192_R	1.281	0.94
159_R	197_Q	1.255	0.93
261_E	265_Q	1.239	0.93
34_N	98_L	1.235	0.92
174_T	179_A	1.229	0.92
66_V	79_G	1.221	0.92
156_M	197_Q	1.215	0.92
254_D	257_A	1.192	0.91
87_Q	91_R	1.190	0.91
188_E	192_R	1.175	0.90
94_D	98_L	1.175	0.90
206_I	220_V	1.170	0.90
194_K	202_T	1.166	0.90
207_M	210_L	1.157	0.90
90_E	132_K	1.139	0.89
174_T	182_T	1.134	0.89
42_E	65_S	1.128	0.88
68_T	81_P	1.121	0.88
16_I	49_H	1.121	0.88
257_A	261_E	1.115	0.88
193_A	200_I	1.096	0.87
94_D	132_K	1.094	0.87
110_A	185_R	1.090	0.87
8_L	250_Y	1.089	0.87
224_L	232_M	1.078	0.86
208_I	217_I	1.077	0.86
108_A	122_F	1.076	0.86
218_I	266_K	1.063	0.85
164_N	205_S	1.056	0.85
165_H	186_S	1.046	0.84
56_R	99_M	1.041	0.84
218_I	222_D	1.040	0.84
35_N	91_R	1.033	0.84
150_D	153_K	1.021	0.83
260_K	273_A	1.019	0.83
52_W	78_T	1.018	0.83
156_M	196_M	1.018	0.83
37_H	65_S	1.015	0.83
251_Y	255_E	1.009	0.82
66_V	77_K	1.002	0.82
241_T	244_H	0.999	0.82
219_E	223_D	0.994	0.81
149_Y	188_E	0.992	0.81
222_D	226_A	0.989	0.81
192_R	196_M	0.987	0.81
66_V	82_T	0.986	0.81
156_M	163_L	0.985	0.81
62_I	125_T	0.982	0.80
130_R	160_P	0.981	0.80
97_A	133_S	0.980	0.80
217_I	251_Y	0.978	0.80
214_K	218_I	0.975	0.80
124_E	128_A	0.973	0.80
217_I	249_K	0.963	0.79
24_Y	52_W	0.959	0.79
73_F	174_T	0.953	0.78
176_R	248_Q	0.949	0.78
178_R	181_A	0.945	0.78
10_K	44_K	0.945	0.78
155_L	159_R	0.940	0.77
156_M	200_I	0.938	0.77
28_K	41_E	0.936	0.77
152_L	192_R	0.936	0.77
26_G	56_R	0.932	0.77
101_L	104_A	0.920	0.76
129_I	133_S	0.915	0.75
123_A	155_L	0.913	0.75
140_V	160_P	0.907	0.75
255_E	258_E	0.902	0.74
96_V	136_T	0.901	0.74
23_N	56_R	0.883	0.73
272_E	282_H	0.883	0.73
174_T	180_R	0.881	0.73
120_G	154_T	0.874	0.72
218_I	258_E	0.866	0.71
147_G	185_R	0.866	0.71
140_V	164_N	0.866	0.71
179_A	205_S	0.865	0.71
230_D	269_S	0.865	0.71
221_M	262_I	0.863	0.71
56_R	100_N	0.858	0.71
149_Y	152_L	0.854	0.70
12_E	16_I	0.854	0.70
18_L	49_H	0.852	0.70
93_A	132_K	0.850	0.70
222_D	262_I	0.848	0.70
27_L	53_A	0.847	0.70
75_A	241_T	0.846	0.70
60_F	92_V	0.838	0.69
191_R	227_N	0.834	0.68
78_T	110_A	0.822	0.67
9_R	12_E	0.819	0.67
27_L	99_M	0.817	0.67
204_S	234_I	0.811	0.66
143_S	155_L	0.811	0.66
142_P	155_L	0.809	0.66
127_R	157_D	0.809	0.66
42_E	75_A	0.808	0.66
225_L	230_D	0.807	0.66
84_L	121_I	0.805	0.66
125_T	129_I	0.803	0.66
174_T	181_A	0.802	0.65
191_R	228_N	0.800	0.65
167_I	220_V	0.798	0.65
104_A	136_T	0.796	0.65
96_V	104_A	0.795	0.65
123_A	154_T	0.794	0.65
239_Q	250_Y	0.793	0.65
90_E	131_R	0.792	0.64
110_A	174_T	0.790	0.64
61_M	272_E	0.789	0.64
171_R	175_P	0.784	0.64
224_L	227_N	0.783	0.64
48_I	52_W	0.779	0.63
7_H	10_K	0.772	0.62
30_L	34_N	0.771	0.62
252_H	255_E	0.768	0.62
19_N	49_H	0.768	0.62
252_H	257_A	0.767	0.62
31_M	52_W	0.767	0.62
202_T	230_D	0.767	0.62
221_M	266_K	0.766	0.62
215_E	218_I	0.765	0.62
86_L	121_I	0.765	0.62
126_V	138_I	0.763	0.62
75_A	110_A	0.761	0.61
264_M	271_C	0.760	0.61
193_A	197_Q	0.759	0.61
59_T	283_A	0.754	0.61
96_V	129_I	0.752	0.60
258_E	261_E	0.751	0.60
174_T	220_V	0.749	0.60
233_A	277_V	0.743	0.60
270_H	282_H	0.741	0.59
117_G	146_G	0.740	0.59
221_M	225_L	0.739	0.59
214_K	251_Y	0.734	0.59
32_R	42_E	0.727	0.58
108_A	145_M	0.724	0.58
140_V	163_L	0.722	0.57
13_W	253_P	0.719	0.57
191_R	226_A	0.717	0.57
206_I	217_I	0.717	0.57
152_L	189_F	0.716	0.57
146_G	180_R	0.713	0.56
37_H	82_T	0.712	0.56
174_T	184_D	0.711	0.56
102_K	284_D	0.711	0.56
149_Y	153_K	0.709	0.56
174_T	205_S	0.709	0.56
137_T	161_D	0.706	0.56
52_W	174_T	0.706	0.56
218_I	265_Q	0.705	0.56
272_E	286_Q	0.705	0.56
146_G	151_N	0.702	0.55
163_L	189_F	0.699	0.55
231_I	286_Q	0.697	0.55
110_A	145_M	0.696	0.55
110_A	229_V	0.695	0.54
10_K	238_L	0.695	0.54
142_P	193_A	0.694	0.54
245_L	248_Q	0.691	0.54
204_S	227_N	0.688	0.54
167_I	186_S	0.681	0.53
152_L	163_L	0.678	0.53
14_L	276_L	0.677	0.53
155_L	193_A	0.675	0.52
17_K	23_N	0.674	0.52
183_Y	219_E	0.673	0.52
140_V	158_T	0.673	0.52
234_I	259_L	0.672	0.52
164_N	282_H	0.672	0.52
142_P	145_M	0.671	0.52
41_E	48_I	0.668	0.52
155_L	158_T	0.668	0.52
169_T	208_I	0.667	0.51
29_K	33_E	0.666	0.51
70_A	78_T	0.666	0.51
221_M	268_F	0.666	0.51
70_A	110_A	0.665	0.51
93_A	129_I	0.663	0.51
201_P	231_I	0.663	0.51
164_N	179_A	0.661	0.51
127_R	158_T	0.652	0.50
70_A	180_R	0.650	0.50
270_H	286_Q	0.649	0.50
22_E	26_G	0.647	0.49
106_I	140_V	0.646	0.49
219_E	222_D	0.646	0.49
210_L	245_L	0.645	0.49
122_F	164_N	0.644	0.49
130_R	161_D	0.644	0.49
222_D	265_Q	0.642	0.49
60_F	104_A	0.641	0.49
215_E	225_L	0.640	0.49
213_T	248_Q	0.639	0.48
187_L	227_N	0.637	0.48
130_R	163_L	0.637	0.48
263_A	272_E	0.636	0.48
181_A	207_M	0.635	0.48
42_E	122_F	0.634	0.48
249_K	259_L	0.634	0.48
257_A	264_M	0.632	0.48
17_K	20_T	0.632	0.48
124_E	129_I	0.630	0.47
37_H	41_E	0.629	0.47
121_I	272_E	0.628	0.47
156_M	194_K	0.627	0.47
260_K	263_A	0.627	0.47
142_P	189_F	0.624	0.47
41_E	110_A	0.623	0.47
52_W	182_T	0.623	0.47
105_V	235_G	0.623	0.47
217_I	234_I	0.621	0.47
7_H	239_Q	0.620	0.46
22_E	25_T	0.620	0.46
21_N	24_Y	0.617	0.46
213_T	216_E	0.616	0.46
12_E	254_D	0.616	0.46
171_R	182_T	0.615	0.46
16_I	19_N	0.614	0.46
208_I	251_Y	0.612	0.46
244_H	279_S	0.611	0.45
205_S	282_H	0.611	0.45
232_M	263_A	0.608	0.45
169_T	177_V	0.607	0.45
152_L	196_M	0.605	0.45
18_L	44_K	0.602	0.45
163_L	202_T	0.602	0.45
225_L	232_M	0.602	0.45
179_A	182_T	0.601	0.44
10_K	16_I	0.599	0.44
15_K	274_G	0.596	0.44
167_I	204_S	0.595	0.44
172_R	238_L	0.593	0.44
23_N	53_A	0.592	0.43
76_V	282_H	0.592	0.43
10_K	17_K	0.591	0.43
187_L	223_D	0.591	0.43
180_R	205_S	0.590	0.43
256_F	273_A	0.588	0.43
178_R	207_M	0.587	0.43
75_A	78_T	0.587	0.43
94_D	97_A	0.586	0.43
171_R	179_A	0.586	0.43
169_T	173_L	0.583	0.43
172_R	219_E	0.582	0.42
193_A	201_P	0.581	0.42
261_E	264_M	0.580	0.42
159_R	193_A	0.580	0.42
61_M	110_A	0.580	0.42
16_I	48_I	0.579	0.42
90_E	124_E	0.578	0.42
154_T	159_R	0.577	0.42
24_Y	27_L	0.575	0.42
239_Q	242_K	0.572	0.41
252_H	273_A	0.572	0.41
205_S	220_V	0.568	0.41
167_I	206_I	0.568	0.41
140_V	205_S	0.568	0.41
72_R	75_A	0.567	0.41
34_N	99_M	0.567	0.41
140_V	145_M	0.565	0.41
118_G	143_S	0.565	0.41
174_T	189_F	0.563	0.40
102_K	129_I	0.562	0.40
189_F	192_R	0.560	0.40
35_N	87_Q	0.559	0.40
231_I	272_E	0.559	0.40
216_E	219_E	0.558	0.40
130_R	159_R	0.558	0.40
157_D	196_M	0.557	0.40
28_K	48_I	0.556	0.40
164_N	233_A	0.555	0.40
65_S	82_T	0.552	0.39
167_I	183_Y	0.552	0.39
103_H	138_I	0.552	0.39
72_R	180_R	0.550	0.39
238_L	250_Y	0.546	0.39
24_Y	229_V	0.546	0.39
217_I	259_L	0.545	0.39
284_D	287_V	0.545	0.39
210_L	248_Q	0.544	0.38
63_L	108_A	0.544	0.38
79_G	82_T	0.544	0.38
217_I	221_M	0.543	0.38
39_V	179_A	0.541	0.38
30_L	91_R	0.540	0.38
34_N	91_R	0.539	0.38
177_V	207_M	0.539	0.38
155_L	160_P	0.536	0.38
60_F	99_M	0.533	0.37
253_P	275_P	0.533	0.37
95_S	98_L	0.533	0.37
151_N	154_T	0.532	0.37
130_R	164_N	0.531	0.37
15_K	259_L	0.530	0.37
75_A	99_M	0.530	0.37
162_I	179_A	0.530	0.37
263_A	286_Q	0.529	0.37
106_I	125_T	0.528	0.37
214_K	262_I	0.527	0.37
44_K	70_A	0.526	0.37
52_W	229_V	0.525	0.37
12_E	25_T	0.525	0.37
55_R	282_H	0.525	0.37
149_Y	185_R	0.525	0.37
219_E	261_E	0.523	0.36
27_L	31_M	0.522	0.36
73_F	167_I	0.522	0.36
120_G	123_A	0.522	0.36
231_I	239_Q	0.520	0.36
97_A	222_D	0.519	0.36
86_L	120_G	0.518	0.36
108_A	174_T	0.518	0.36
39_V	76_V	0.518	0.36
123_A	157_D	0.517	0.36
153_K	263_A	0.517	0.36
142_P	229_V	0.516	0.36
92_V	104_A	0.516	0.36
44_K	243_K	0.515	0.36
137_T	287_V	0.515	0.36
24_Y	31_M	0.515	0.36
34_N	94_D	0.513	0.35
160_P	164_N	0.513	0.35
215_E	254_D	0.512	0.35
23_N	27_L	0.508	0.35
122_F	143_S	0.508	0.35
110_A	113_D	0.507	0.35
188_E	195_E	0.506	0.35
77_K	239_Q	0.505	0.35
172_R	183_Y	0.502	0.34
10_K	142_P	0.502	0.34
61_M	106_I	0.501	0.34
222_D	225_L	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	0.8926	100	0.642	Contact Map
4wcxA	1	0.9329	99.7	0.877	Contact Map
4r33A	2	0.9631	99.7	0.879	Contact Map
4rtbA	2	0.9463	99.7	0.88	Contact Map
3t7vA	1	0.9094	99.7	0.881	Contact Map
1r30A	2	0.9027	99.6	0.883	Contact Map
3iixA	1	0.8993	99.6	0.884	Contact Map
1oltA	1	0.9094	99.5	0.895	Contact Map
2qgqA	1	0.7383	99.5	0.895	Contact Map
4jc0A	1	0.9564	99.4	0.901	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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