MSBB - ECOLI - GREMLIN Contacts

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MSBB - Lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase

UniProt:	P24205	Sequences: METKKNNSEYIPEFDKSFRHPRYWGAWLGVAAMAGIALTPPKFRDPILARLGRFAGRLGKSSRRRALINLSLCFPERSEAEREAIVDEMFATAPQAMAMMAELAIRGPEKIQPRVDWQGLEIIEEMRRNNEKVIFLVPHGWAVDIPAMLMASQGQKMAAMFHNQGNPVFDYVWNTVRRRFGGRLHARNDGIKPFIQSVRQGYWGYYLPDQDHGPEHSEFVDFFATYKATLPAIGRLMKVCRARVVPLFPIYDGKTHRLTIQVRPPMDDLLEADDHTIARRMNEEVEIFVGPRPEQYTWILKLLKTRKPGEIQPYKRKDLYPIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10614
Length:	323 (283)
Sequences:	4326 (3076)
Seq/√Len:	182.9

ECOLI - MSBB HTRB DDG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
279_R	283_E	3.947	1.00
118_Q	259_T	3.888	1.00
116_D	259_T	3.681	1.00
118_Q	261_Q	3.355	1.00
252_D	259_T	2.940	1.00
88_E	294_E	2.847	1.00
67_L	86_V	2.821	1.00
67_L	83_E	2.819	1.00
78_S	81_E	2.781	1.00
221_D	279_R	2.758	1.00
221_D	226_Y	2.747	1.00
122_I	264_P	2.723	1.00
53_R	91_A	2.713	1.00
120_L	124_E	2.608	1.00
77_R	81_E	2.579	1.00
283_E	286_E	2.567	1.00
76_E	290_G	2.469	1.00
70_L	82_R	2.459	1.00
124_E	128_R	2.321	1.00
119_G	122_I	2.318	1.00
48_L	94_P	2.309	1.00
229_T	282_N	2.262	1.00
71_S	82_R	2.260	1.00
197_S	202_Y	2.127	1.00
158_A	202_Y	2.117	1.00
40_P	43_F	2.110	1.00
275_H	279_R	2.082	1.00
263_R	284_E	2.076	1.00
72_L	225_T	2.066	1.00
121_E	125_E	2.061	1.00
77_R	85_I	2.060	1.00
65_R	301_K	2.033	1.00
122_I	125_E	2.000	1.00
223_F	286_E	1.990	1.00
246_P	263_R	1.951	1.00
250_I	259_T	1.931	1.00
68_I	71_S	1.927	1.00
250_I	292_R	1.895	1.00
71_S	79_E	1.862	1.00
74_F	77_R	1.857	1.00
163_N	186_A	1.846	1.00
246_P	265_P	1.809	1.00
49_A	91_A	1.792	1.00
99_M	251_Y	1.791	1.00
171_Y	175_T	1.771	1.00
131_E	243_R	1.771	1.00
219_F	226_Y	1.765	1.00
116_D	257_R	1.741	1.00
273_D	276_T	1.708	1.00
66_A	86_V	1.702	1.00
220_V	279_R	1.698	1.00
220_V	282_N	1.637	1.00
138_P	285_V	1.636	1.00
218_E	278_A	1.618	1.00
126_M	245_V	1.588	1.00
56_G	63_R	1.568	1.00
250_I	261_Q	1.545	1.00
284_E	287_I	1.521	1.00
125_E	129_N	1.515	1.00
122_I	245_V	1.514	1.00
195_I	199_R	1.501	1.00
84_A	88_E	1.466	1.00
81_E	84_A	1.449	1.00
110_K	114_R	1.446	1.00
245_V	262_V	1.433	1.00
158_A	197_S	1.424	1.00
67_L	71_S	1.408	1.00
263_R	287_I	1.403	1.00
225_T	306_R	1.387	1.00
194_F	204_G	1.378	1.00
66_A	89_M	1.375	1.00
280_R	284_E	1.369	1.00
48_L	52_G	1.366	1.00
81_E	85_I	1.365	1.00
162_H	165_G	1.364	1.00
34_A	38_L	1.361	1.00
131_E	241_R	1.349	1.00
183_R	193_P	1.337	1.00
49_A	95_Q	1.336	1.00
67_L	82_R	1.332	1.00
64_R	68_I	1.326	1.00
108_P	112_Q	1.317	1.00
286_E	290_G	1.305	1.00
77_R	82_R	1.298	1.00
221_D	283_E	1.285	1.00
54_F	58_L	1.284	1.00
42_K	46_P	1.265	1.00
174_N	178_R	1.262	1.00
44_R	98_A	1.257	1.00
223_F	290_G	1.244	1.00
246_P	266_M	1.238	1.00
134_I	242_A	1.232	1.00
73_C	303_L	1.231	1.00
253_G	256_H	1.223	1.00
135_F	247_L	1.219	1.00
219_F	228_A	1.216	1.00
56_G	87_D	1.209	1.00
248_F	288_F	1.209	1.00
170_D	174_N	1.190	1.00
274_D	278_A	1.184	1.00
280_R	283_E	1.183	1.00
285_V	289_V	1.181	1.00
252_D	257_R	1.178	1.00
106_R	110_K	1.177	1.00
269_L	272_A	1.172	1.00
125_E	128_R	1.167	1.00
196_Q	200_Q	1.156	1.00
160_M	194_F	1.147	1.00
234_G	278_A	1.146	1.00
63_R	67_L	1.145	1.00
133_V	203_W	1.145	1.00
183_R	202_Y	1.140	1.00
248_F	263_R	1.131	1.00
112_Q	152_S	1.129	1.00
271_E	277_I	1.129	1.00
211_D	305_T	1.125	1.00
237_M	244_V	1.122	1.00
251_Y	295_Q	1.120	1.00
60_K	63_R	1.119	1.00
133_V	243_R	1.118	1.00
50_R	54_F	1.115	1.00
85_I	294_E	1.114	1.00
56_G	86_V	1.111	1.00
46_P	50_R	1.107	1.00
253_G	257_R	1.102	1.00
41_P	45_D	1.098	1.00
219_F	307_K	1.092	1.00
161_F	184_L	1.085	1.00
218_E	275_H	1.085	1.00
261_Q	291_P	1.077	1.00
210_Q	300_L	1.064	1.00
46_P	49_A	1.064	1.00
158_A	185_H	1.056	1.00
124_E	127_R	1.048	1.00
287_I	290_G	1.047	1.00
193_P	196_Q	1.044	1.00
160_M	206_Y	1.043	1.00
122_I	126_M	1.031	1.00
60_K	64_R	1.029	1.00
226_Y	307_K	1.028	1.00
246_P	284_E	1.027	1.00
63_R	90_F	1.025	1.00
116_D	252_D	1.019	0.99
272_A	277_I	1.017	0.99
30_V	34_A	1.014	0.99
292_R	295_Q	1.008	0.99
248_F	284_E	1.004	0.99
238_K	277_I	1.001	0.99
66_A	299_I	1.000	0.99
74_F	82_R	0.998	0.99
136_L	281_M	0.992	0.99
45_D	95_Q	0.991	0.99
42_K	45_D	0.990	0.99
92_T	95_Q	0.972	0.99
227_K	302_L	0.966	0.99
272_A	276_T	0.962	0.99
122_I	265_P	0.955	0.99
70_L	86_V	0.951	0.99
129_N	243_R	0.951	0.99
208_P	233_I	0.948	0.99
192_K	195_I	0.948	0.99
147_A	159_A	0.944	0.99
30_V	172_V	0.939	0.99
288_F	291_P	0.934	0.99
53_R	87_D	0.931	0.99
189_D	193_P	0.926	0.99
132_K	242_A	0.924	0.99
93_A	299_I	0.923	0.99
130_N	201_G	0.923	0.99
34_A	37_A	0.923	0.99
263_R	288_F	0.910	0.99
164_Q	173_W	0.910	0.99
135_F	203_W	0.909	0.99
43_F	46_P	0.909	0.99
283_E	287_I	0.909	0.99
298_W	302_L	0.907	0.99
73_C	223_F	0.906	0.99
57_R	83_E	0.895	0.99
126_M	129_N	0.891	0.99
68_I	72_L	0.879	0.99
44_R	102_E	0.862	0.98
57_R	87_D	0.860	0.98
219_F	305_T	0.860	0.98
210_Q	298_W	0.859	0.98
89_M	299_I	0.858	0.98
218_E	231_P	0.853	0.98
92_T	294_E	0.843	0.98
40_P	46_P	0.843	0.98
127_R	201_G	0.843	0.98
39_T	43_F	0.841	0.98
70_L	77_R	0.838	0.98
144_D	177_R	0.835	0.98
62_S	300_L	0.834	0.98
138_P	208_P	0.826	0.98
114_R	257_R	0.824	0.98
143_V	207_L	0.821	0.98
125_E	264_P	0.819	0.98
69_N	289_V	0.819	0.98
107_G	110_K	0.818	0.98
126_M	243_R	0.817	0.98
210_Q	297_T	0.816	0.98
89_M	93_A	0.815	0.98
140_G	295_Q	0.814	0.98
276_T	280_R	0.813	0.98
158_A	183_R	0.813	0.98
284_E	288_F	0.806	0.97
212_H	230_L	0.797	0.97
218_E	279_R	0.796	0.97
211_D	219_F	0.791	0.97
45_D	49_A	0.791	0.97
117_W	120_L	0.784	0.97
227_K	303_L	0.779	0.97
221_D	224_A	0.777	0.97
136_L	208_P	0.775	0.97
56_G	83_E	0.774	0.97
183_R	197_S	0.772	0.97
243_R	265_P	0.768	0.96
117_W	149_L	0.768	0.96
238_K	274_D	0.761	0.96
276_T	279_R	0.760	0.96
296_Y	303_L	0.757	0.96
254_K	257_R	0.754	0.96
70_L	85_I	0.751	0.96
251_Y	258_L	0.750	0.96
195_I	239_V	0.748	0.96
210_Q	302_L	0.746	0.96
33_M	101_A	0.746	0.96
263_R	291_P	0.745	0.96
233_I	281_M	0.744	0.96
264_P	267_D	0.744	0.96
268_D	271_E	0.744	0.96
238_K	272_A	0.741	0.96
217_S	228_A	0.738	0.96
270_L	277_I	0.734	0.95
110_K	113_P	0.732	0.95
92_T	251_Y	0.732	0.95
214_P	305_T	0.731	0.95
26_A	30_V	0.719	0.95
277_I	280_R	0.718	0.95
72_L	303_L	0.716	0.95
140_G	288_F	0.715	0.95
68_I	225_T	0.714	0.95
63_R	86_V	0.712	0.95
132_K	198_V	0.711	0.95
59_G	62_S	0.711	0.95
220_V	278_A	0.708	0.95
56_G	67_L	0.704	0.94
50_R	53_R	0.703	0.94
269_L	277_I	0.698	0.94
57_R	60_K	0.696	0.94
52_G	56_G	0.693	0.94
62_S	65_R	0.693	0.94
69_N	223_F	0.687	0.94
219_F	306_R	0.687	0.94
167_P	171_Y	0.686	0.94
94_P	97_M	0.683	0.93
79_E	83_E	0.681	0.93
119_G	264_P	0.681	0.93
142_A	296_Y	0.679	0.93
287_I	291_P	0.677	0.93
52_G	91_A	0.676	0.93
38_L	43_F	0.676	0.93
138_P	281_M	0.674	0.93
88_E	91_A	0.674	0.93
228_A	305_T	0.673	0.93
192_K	235_R	0.672	0.93
185_H	197_S	0.671	0.93
65_R	300_L	0.667	0.93
39_T	42_K	0.665	0.92
234_G	238_K	0.665	0.92
300_L	304_K	0.664	0.92
37_A	105_I	0.663	0.92
194_F	236_L	0.661	0.92
26_A	168_V	0.659	0.92
223_F	289_V	0.658	0.92
53_R	57_R	0.658	0.92
140_G	292_R	0.657	0.92
93_A	297_T	0.656	0.92
27_W	31_A	0.655	0.92
193_P	197_S	0.655	0.92
56_G	90_F	0.654	0.92
212_H	228_A	0.650	0.92
229_T	302_L	0.650	0.92
65_R	69_N	0.649	0.92
161_F	186_A	0.648	0.91
41_P	102_E	0.645	0.91
39_T	47_I	0.645	0.91
234_G	277_I	0.644	0.91
156_K	202_Y	0.644	0.91
164_Q	170_D	0.640	0.91
278_A	282_N	0.640	0.91
233_I	244_V	0.637	0.91
53_R	56_G	0.634	0.91
265_P	280_R	0.634	0.91
83_E	86_V	0.633	0.91
146_P	205_Y	0.631	0.90
134_I	240_C	0.629	0.90
95_Q	251_Y	0.626	0.90
197_S	204_G	0.626	0.90
35_G	38_L	0.626	0.90
246_P	288_F	0.624	0.90
123_I	135_F	0.622	0.90
134_I	206_Y	0.621	0.90
40_P	44_R	0.621	0.90
143_V	205_Y	0.616	0.89
248_F	291_P	0.615	0.89
55_A	90_F	0.615	0.89
217_S	220_V	0.613	0.89
28_L	31_A	0.611	0.89
161_F	170_D	0.611	0.89
150_M	157_M	0.611	0.89
117_W	262_V	0.610	0.89
237_M	243_R	0.610	0.89
163_N	170_D	0.609	0.89
142_A	210_Q	0.608	0.89
222_F	289_V	0.608	0.89
92_T	295_Q	0.607	0.89
109_E	112_Q	0.607	0.89
211_D	228_A	0.607	0.89
137_V	205_Y	0.607	0.89
108_P	148_M	0.607	0.89
234_G	269_L	0.605	0.88
137_V	146_P	0.604	0.88
121_E	124_E	0.603	0.88
126_M	133_V	0.601	0.88
144_D	205_Y	0.600	0.88
27_W	30_V	0.600	0.88
120_L	123_I	0.599	0.88
235_R	239_V	0.598	0.88
156_K	183_R	0.595	0.88
82_R	85_I	0.595	0.88
230_L	233_I	0.595	0.88
95_Q	99_M	0.594	0.88
93_A	96_A	0.594	0.88
96_A	137_V	0.592	0.87
178_R	184_L	0.589	0.87
208_P	281_M	0.589	0.87
123_I	127_R	0.587	0.87
112_Q	153_Q	0.587	0.87
162_H	212_H	0.587	0.87
50_R	58_L	0.586	0.87
73_C	225_T	0.579	0.86
247_L	262_V	0.579	0.86
136_L	233_I	0.579	0.86
64_R	67_L	0.578	0.86
197_S	200_Q	0.577	0.86
144_D	159_A	0.576	0.86
35_G	39_T	0.575	0.86
132_K	204_G	0.575	0.86
79_E	82_R	0.573	0.86
220_V	275_H	0.573	0.86
252_D	256_H	0.572	0.86
162_H	298_W	0.572	0.86
159_A	184_L	0.569	0.85
89_M	297_T	0.568	0.85
250_I	291_P	0.567	0.85
138_P	248_F	0.567	0.85
52_G	57_R	0.566	0.85
119_G	262_V	0.565	0.85
45_D	48_L	0.564	0.85
141_W	249_P	0.562	0.85
69_N	73_C	0.560	0.84
124_E	153_Q	0.559	0.84
52_G	94_P	0.558	0.84
72_L	223_F	0.557	0.84
266_M	280_R	0.556	0.84
75_P	82_R	0.556	0.84
109_E	113_P	0.553	0.84
90_F	93_A	0.551	0.83
49_A	53_R	0.551	0.83
198_V	204_G	0.550	0.83
69_N	177_R	0.550	0.83
94_P	98_A	0.549	0.83
225_T	305_T	0.549	0.83
41_P	99_M	0.547	0.83
147_A	184_L	0.545	0.83
80_A	84_A	0.545	0.83
87_D	91_A	0.543	0.82
198_V	236_L	0.542	0.82
31_A	35_G	0.540	0.82
160_M	232_A	0.539	0.82
160_M	190_G	0.537	0.82
198_V	242_A	0.536	0.82
47_I	50_R	0.534	0.81
78_S	82_R	0.534	0.81
61_S	65_R	0.534	0.81
249_P	260_I	0.534	0.81
65_R	68_I	0.532	0.81
223_F	281_M	0.532	0.81
231_P	235_R	0.531	0.81
103_L	205_Y	0.529	0.81
204_G	236_L	0.528	0.81
268_D	277_I	0.527	0.81
211_D	304_K	0.527	0.81
123_I	150_M	0.526	0.80
119_G	245_V	0.525	0.80
51_L	88_E	0.524	0.80
117_W	260_I	0.524	0.80
61_S	64_R	0.524	0.80
41_P	44_R	0.519	0.80
118_Q	252_D	0.519	0.80
185_H	193_P	0.519	0.80
126_M	262_V	0.519	0.80
225_T	303_L	0.516	0.79
211_D	230_L	0.515	0.79
132_K	243_R	0.515	0.79
37_A	40_P	0.515	0.79
123_I	133_V	0.514	0.79
192_K	216_H	0.510	0.78
66_A	90_F	0.509	0.78
214_P	308_P	0.508	0.78
206_Y	232_A	0.508	0.78
231_P	274_D	0.508	0.78
198_V	240_C	0.507	0.78
131_E	267_D	0.507	0.78
206_Y	233_I	0.506	0.78
133_V	245_V	0.504	0.78
234_G	303_L	0.504	0.78
208_P	232_A	0.503	0.77
171_Y	174_N	0.502	0.77
102_E	110_K	0.501	0.77
134_I	185_H	0.501	0.77
221_D	286_E	0.500	0.77
47_I	98_A	0.500	0.77

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
1iuqA	1	0.8916	98.2	0.879	Contact Map
3cg0A	4	0.3839	22.8	0.96	Contact Map
2lpmA	1	0.3808	21.6	0.96	Contact Map
3f6pA	1	0.3684	15.1	0.963	Contact Map
4nicA	2	0.3591	14.7	0.963	Contact Map
3j61Z	1	0.3344	14.5	0.963	Contact Map
4ujrM	1	0.3313	14.2	0.963	Contact Map
1xhfA	2	0.3746	13.6	0.964	Contact Map
3to5A	1	0.3839	13.3	0.964	Contact Map
4igaA	1	0.356	13	0.964	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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