UBIF - ECOLI - GREMLIN Contacts

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UBIF - 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase

UniProt:	P75728	Sequences: MTNQPTEIAIVGGGMVGGALALGLAQHGFAVTVIEHAEPAPFVADSQPDVRISAISAASVSLLKGLGVWDAVQAMRCHPYRRLETWEWETAHVVFDAAELKLPLLGYMVENTVLQQALWQALEAHPKVTLRVPGSLIALHRHDDLQELELKGGEVIRAKLVIGADGANSQVRQMAGIGVHAWQYAQSCMLISVQCENDPGDSTWQQFTPDGPRAFLPLFDNWASLVWYDSPARIRQLQNMNMAQLQAEIAKHFPSRLGYVTPLAAGAFPLTRRHALQYVQPGLALVGDAAHTIHPLAGQGVNLGYRDVDALIDVLVNARSYGEAWASYPVLKRYQMRRMADNFIMQSGMDLFYAGFSNNLPPLRFMRNLGLMAAERAGVLKRQALKYALGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13658
Length:	391 (340)
Sequences:	27128 (20758)
Seq/√Len:	1125.7

ECOLI - UBIF UBIH UBII MHPA FIXC YDIS YGCN CBRA
BACSU - YHJG YETM
HALSA - Q9HS01 Q9HS24 Q9HMA0 Q9HQE5
SULSO - Q97V18 Q97V59 Q97ZK8 Q97W83 Q97W89

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_T	131_R	4.167	1.00
36_H	135_S	3.529	1.00
16_V	304_G	3.449	1.00
9_A	158_A	3.424	1.00
7_E	30_A	3.293	1.00
7_E	159_K	3.205	1.00
335_Q	339_M	3.007	1.00
138_A	174_M	2.749	1.00
135_S	151_K	2.740	1.00
27_H	316_V	2.679	1.00
6_T	32_T	2.661	1.00
34_I	156_I	2.618	1.00
147_E	155_V	2.605	1.00
121_A	124_A	2.598	1.00
20_L	162_I	2.520	1.00
23_G	312_I	2.410	1.00
134_G	152_G	2.397	1.00
9_A	34_I	2.357	1.00
147_E	157_R	2.342	1.00
140_H	147_E	2.342	1.00
116_Q	120_Q	2.306	1.00
71_A	120_Q	2.296	1.00
241_N	244_Q	2.246	1.00
138_A	149_E	2.214	1.00
149_E	155_V	2.191	1.00
137_I	151_K	2.130	1.00
16_V	286_V	2.095	1.00
145_L	157_R	2.093	1.00
19_A	305_Y	2.083	1.00
9_A	148_L	2.057	1.00
131_R	134_G	2.046	1.00
163_G	171_V	2.039	1.00
64_K	69_W	2.035	1.00
38_E	133_P	1.920	1.00
134_G	150_L	1.916	1.00
314_V	337_R	1.905	1.00
140_H	149_E	1.875	1.00
8_I	29_F	1.872	1.00
71_A	121_A	1.847	1.00
30_A	129_T	1.845	1.00
7_E	32_T	1.812	1.00
121_A	125_H	1.800	1.00
8_I	24_L	1.798	1.00
142_H	147_E	1.783	1.00
22_L	121_A	1.782	1.00
163_G	285_L	1.781	1.00
62_L	309_D	1.756	1.00
59_S	302_N	1.748	1.00
308_V	312_I	1.745	1.00
242_M	246_Q	1.736	1.00
34_I	150_L	1.729	1.00
314_V	333_R	1.723	1.00
29_F	316_V	1.712	1.00
136_L	148_L	1.701	1.00
339_M	343_F	1.690	1.00
164_A	286_V	1.680	1.00
279_V	332_K	1.670	1.00
150_L	156_I	1.656	1.00
91_A	94_V	1.640	1.00
277_Q	280_Q	1.627	1.00
71_A	74_A	1.621	1.00
141_R	280_Q	1.612	1.00
65_G	309_D	1.601	1.00
25_A	128_V	1.600	1.00
243_A	247_A	1.599	1.00
165_D	169_S	1.596	1.00
244_Q	247_A	1.586	1.00
119_W	132_V	1.581	1.00
279_V	284_A	1.572	1.00
70_D	74_A	1.565	1.00
142_H	157_R	1.562	1.00
71_A	124_A	1.558	1.00
247_A	251_K	1.536	1.00
22_L	26_Q	1.534	1.00
142_H	145_L	1.533	1.00
170_Q	174_M	1.527	1.00
9_A	156_I	1.516	1.00
310_A	314_V	1.509	1.00
247_A	250_A	1.507	1.00
122_L	128_V	1.496	1.00
139_L	161_V	1.490	1.00
21_A	33_V	1.486	1.00
20_L	308_V	1.477	1.00
119_W	123_E	1.471	1.00
32_T	156_I	1.466	1.00
260_V	263_L	1.442	1.00
26_Q	125_H	1.437	1.00
69_W	73_Q	1.431	1.00
310_A	337_R	1.431	1.00
175_A	283_L	1.413	1.00
277_Q	335_Q	1.412	1.00
284_A	311_L	1.399	1.00
278_Y	342_N	1.398	1.00
23_G	66_L	1.392	1.00
11_V	136_L	1.383	1.00
160_L	331_L	1.371	1.00
15_M	301_V	1.369	1.00
278_Y	335_Q	1.340	1.00
75_M	113_V	1.340	1.00
307_D	338_R	1.331	1.00
25_A	125_H	1.327	1.00
59_S	305_Y	1.321	1.00
162_I	286_V	1.312	1.00
306_R	341_D	1.301	1.00
11_V	165_D	1.293	1.00
314_V	330_V	1.293	1.00
131_R	156_I	1.290	1.00
246_Q	250_A	1.287	1.00
313_D	337_R	1.271	1.00
6_T	9_A	1.269	1.00
170_Q	173_Q	1.255	1.00
120_Q	123_E	1.251	1.00
140_H	155_V	1.245	1.00
22_L	122_L	1.240	1.00
70_D	73_Q	1.238	1.00
291_H	307_D	1.236	1.00
40_A	132_V	1.235	1.00
22_L	125_H	1.230	1.00
10_I	20_L	1.222	1.00
148_L	158_A	1.220	1.00
134_G	154_E	1.217	1.00
136_L	171_V	1.216	1.00
32_T	129_T	1.214	1.00
257_L	260_V	1.209	1.00
20_L	24_L	1.206	1.00
272_R	350_D	1.204	1.00
137_I	149_E	1.202	1.00
279_V	335_Q	1.192	1.00
136_L	139_L	1.184	1.00
259_Y	262_P	1.168	1.00
9_A	32_T	1.154	1.00
243_A	246_Q	1.154	1.00
75_M	116_Q	1.151	1.00
314_V	317_N	1.148	1.00
113_V	116_Q	1.148	1.00
19_A	66_L	1.134	1.00
162_I	284_A	1.126	1.00
285_L	289_A	1.119	1.00
11_V	171_V	1.118	1.00
141_R	282_G	1.111	1.00
92_H	95_F	1.109	1.00
167_A	292_T	1.106	1.00
110_E	113_V	1.105	1.00
139_L	174_M	1.105	1.00
194_Q	261_T	1.088	1.00
34_I	131_R	1.085	1.00
178_G	276_L	1.084	1.00
180_H	276_L	1.080	1.00
33_V	130_L	1.078	1.00
240_M	244_Q	1.077	1.00
53_S	301_V	1.075	1.00
326_A	329_P	1.074	1.00
71_A	117_A	1.066	1.00
254_P	257_L	1.066	1.00
10_I	21_A	1.060	1.00
6_T	30_A	1.059	1.00
26_Q	121_A	1.057	1.00
146_Q	282_G	1.050	1.00
293_I	303_L	1.047	1.00
158_A	161_V	1.042	1.00
141_R	146_Q	1.041	1.00
60_V	69_W	1.038	1.00
20_L	286_V	1.028	1.00
194_Q	222_W	1.022	1.00
13_G	18_G	1.019	1.00
6_T	129_T	1.016	1.00
7_E	29_F	1.015	1.00
25_A	127_K	1.013	1.00
84_E	92_H	1.010	1.00
248_E	252_H	1.009	1.00
279_V	328_Y	1.009	1.00
214_A	226_V	1.007	1.00
21_A	31_V	1.005	1.00
19_A	23_G	1.004	1.00
343_F	347_S	1.004	1.00
120_Q	124_A	0.998	1.00
65_G	313_D	0.998	1.00
18_G	122_L	0.994	1.00
31_V	128_V	0.990	1.00
39_P	132_V	0.988	1.00
136_L	170_Q	0.988	1.00
119_W	130_L	0.986	1.00
68_V	121_A	0.983	1.00
71_A	75_M	0.982	1.00
273_R	292_T	0.981	1.00
332_K	336_M	0.975	1.00
270_L	273_R	0.974	1.00
286_V	334_Y	0.972	1.00
257_L	261_T	0.966	1.00
233_R	236_Q	0.959	1.00
146_Q	150_L	0.957	1.00
10_I	31_V	0.955	1.00
255_S	258_G	0.951	1.00
139_L	175_A	0.951	1.00
34_I	134_G	0.950	1.00
82_R	202_S	0.947	1.00
310_A	313_D	0.946	1.00
248_E	251_K	0.933	1.00
40_A	119_W	0.933	1.00
293_I	346_Q	0.924	1.00
163_G	283_L	0.919	1.00
284_A	334_Y	0.918	1.00
350_D	354_A	0.916	1.00
317_N	333_R	0.911	1.00
117_A	120_Q	0.907	1.00
11_V	161_V	0.905	1.00
333_R	336_M	0.905	1.00
254_P	258_G	0.904	1.00
75_M	117_A	0.903	1.00
24_L	29_F	0.901	1.00
15_M	305_Y	0.900	1.00
275_A	285_L	0.897	1.00
194_Q	221_N	0.893	1.00
53_S	111_N	0.892	1.00
32_T	158_A	0.892	1.00
146_Q	161_V	0.891	1.00
261_T	264_A	0.888	1.00
191_I	225_L	0.887	1.00
265_A	268_F	0.886	1.00
280_Q	283_L	0.886	1.00
117_A	121_A	0.882	1.00
28_G	31_V	0.881	1.00
224_S	228_Y	0.881	1.00
25_A	122_L	0.879	1.00
125_H	128_V	0.877	1.00
136_L	174_M	0.875	1.00
22_L	66_L	0.874	1.00
29_F	319_R	0.870	1.00
61_S	64_K	0.870	1.00
23_G	27_H	0.867	1.00
328_Y	332_K	0.865	1.00
72_V	114_L	0.865	1.00
18_G	119_W	0.860	1.00
72_V	117_A	0.858	1.00
244_Q	248_E	0.856	1.00
237_L	241_N	0.853	1.00
68_V	117_A	0.853	1.00
188_C	192_S	0.850	1.00
58_A	306_R	0.849	1.00
94_V	98_A	0.846	1.00
58_A	299_Q	0.845	1.00
148_L	161_V	0.844	1.00
259_Y	263_L	0.843	1.00
123_E	129_T	0.841	1.00
246_Q	261_T	0.834	1.00
58_A	61_S	0.831	1.00
77_C	107_Y	0.830	1.00
60_V	107_Y	0.828	1.00
18_G	115_Q	0.823	1.00
25_A	31_V	0.817	1.00
51_R	111_N	0.815	1.00
34_I	158_A	0.815	1.00
188_C	191_I	0.813	1.00
7_E	158_A	0.807	1.00
24_L	312_I	0.806	1.00
309_D	313_D	0.804	1.00
141_R	281_P	0.803	1.00
269_P	272_R	0.802	1.00
81_R	201_D	0.802	1.00
171_V	283_L	0.800	1.00
259_Y	264_A	0.796	1.00
13_G	35_E	0.795	1.00
177_I	275_A	0.794	1.00
139_L	171_V	0.793	1.00
195_C	198_D	0.793	1.00
25_A	123_E	0.793	1.00
54_A	106_G	0.792	1.00
312_I	316_V	0.791	1.00
203_T	206_Q	0.790	1.00
297_A	349_M	0.790	1.00
258_G	262_P	0.785	1.00
93_V	97_A	0.782	1.00
258_G	261_T	0.782	1.00
327_S	330_V	0.780	1.00
285_L	290_A	0.779	1.00
23_G	26_Q	0.778	1.00
35_E	132_V	0.775	1.00
269_P	273_R	0.774	1.00
94_V	97_A	0.774	1.00
245_L	253_F	0.772	1.00
279_V	331_L	0.768	1.00
50_V	53_S	0.765	1.00
249_I	253_F	0.765	1.00
249_I	252_H	0.764	1.00
162_I	311_L	0.764	1.00
64_K	73_Q	0.763	1.00
278_Y	290_A	0.762	1.00
63_L	305_Y	0.759	1.00
160_L	284_A	0.759	1.00
122_L	127_K	0.755	1.00
111_N	115_Q	0.755	1.00
318_A	333_R	0.754	1.00
21_A	122_L	0.749	1.00
24_L	315_L	0.747	1.00
54_A	108_M	0.747	1.00
123_E	127_K	0.745	1.00
139_L	283_L	0.744	1.00
327_S	331_L	0.742	1.00
221_N	224_S	0.741	1.00
333_R	337_R	0.741	1.00
274_H	343_F	0.741	1.00
189_M	192_S	0.738	1.00
34_I	148_L	0.735	1.00
122_L	125_H	0.729	1.00
109_V	114_L	0.729	1.00
245_L	249_I	0.728	1.00
253_F	256_R	0.728	1.00
84_E	202_S	0.727	1.00
21_A	128_V	0.725	1.00
115_Q	119_W	0.724	1.00
293_I	297_A	0.722	1.00
7_E	156_I	0.721	1.00
195_C	223_A	0.720	1.00
278_Y	339_M	0.719	1.00
27_H	312_I	0.719	1.00
23_G	62_L	0.714	1.00
292_T	307_D	0.713	1.00
184_Y	350_D	0.713	1.00
63_L	68_V	0.711	1.00
60_V	64_K	0.709	1.00
79_P	105_L	0.709	1.00
169_S	172_R	0.708	1.00
19_A	118_L	0.707	1.00
260_V	264_A	0.704	1.00
8_I	160_L	0.701	1.00
110_E	219_F	0.700	1.00
202_S	205_Q	0.699	1.00
176_G	179_V	0.698	1.00
337_R	340_A	0.692	1.00
268_F	271_T	0.692	1.00
275_A	278_Y	0.687	1.00
242_M	265_A	0.686	1.00
230_S	233_R	0.685	1.00
37_A	47_Q	0.679	1.00
204_W	207_F	0.678	1.00
303_L	342_N	0.678	1.00
194_Q	197_N	0.675	1.00
225_L	228_Y	0.674	1.00
92_H	96_D	0.672	1.00
62_L	66_L	0.672	1.00
86_W	204_W	0.670	1.00
122_L	130_L	0.670	1.00
177_I	280_Q	0.669	1.00
342_N	346_Q	0.669	1.00
163_G	169_S	0.667	1.00
316_V	320_S	0.667	1.00
31_V	127_K	0.665	1.00
340_A	344_I	0.664	1.00
195_C	199_P	0.658	1.00
23_G	309_D	0.657	1.00
59_S	62_L	0.657	1.00
113_V	219_F	0.654	1.00
241_N	245_L	0.654	1.00
135_S	170_Q	0.652	1.00
20_L	312_I	0.651	1.00
8_I	20_L	0.651	1.00
237_L	240_M	0.649	1.00
250_A	254_P	0.649	1.00
270_L	294_H	0.648	1.00
281_P	328_Y	0.646	1.00
299_Q	303_L	0.646	1.00
257_L	264_A	0.645	1.00
13_G	33_V	0.642	1.00
58_A	341_D	0.638	1.00
171_V	174_M	0.638	1.00
332_K	335_Q	0.638	1.00
25_A	129_T	0.637	1.00
301_V	304_G	0.636	1.00
31_V	122_L	0.635	1.00
96_D	99_E	0.633	1.00
301_V	305_Y	0.631	1.00
262_P	265_A	0.631	1.00
175_A	280_Q	0.631	1.00
225_L	229_D	0.630	1.00
75_M	109_V	0.629	1.00
172_R	285_L	0.627	1.00
329_P	333_R	0.627	1.00
90_T	93_V	0.625	1.00
18_G	33_V	0.623	1.00
150_L	154_E	0.621	1.00
203_T	207_F	0.621	1.00
22_L	25_A	0.620	1.00
344_I	347_S	0.619	1.00
145_L	159_K	0.618	1.00
56_S	302_N	0.617	1.00
286_V	308_V	0.616	1.00
110_E	222_W	0.615	1.00
150_L	153_G	0.615	1.00
64_K	70_D	0.615	1.00
84_E	87_E	0.609	1.00
95_F	98_A	0.609	1.00
303_L	345_M	0.607	1.00
187_S	231_P	0.603	1.00
326_A	330_V	0.603	1.00
296_L	353_Y	0.603	1.00
293_I	349_M	0.602	1.00
256_R	263_L	0.601	1.00
22_L	128_V	0.598	1.00
163_G	170_Q	0.597	1.00
274_H	278_Y	0.595	1.00
299_Q	302_N	0.595	1.00
196_E	221_N	0.595	1.00
254_P	259_Y	0.594	1.00
160_L	315_L	0.594	1.00
246_Q	252_H	0.588	1.00
139_L	146_Q	0.587	1.00
256_R	264_A	0.586	1.00
255_S	259_Y	0.584	1.00
250_A	257_L	0.584	1.00
160_L	319_R	0.583	1.00
318_A	329_P	0.582	1.00
294_H	297_A	0.581	1.00
179_V	273_R	0.581	1.00
161_V	283_L	0.580	1.00
131_R	154_E	0.580	1.00
134_G	151_K	0.575	1.00
186_Q	190_L	0.572	1.00
64_K	104_L	0.572	1.00
40_A	115_Q	0.570	1.00
38_E	132_V	0.570	1.00
352_F	355_G	0.570	1.00
351_L	354_A	0.569	1.00
274_H	339_M	0.569	1.00
318_A	330_V	0.568	1.00
69_W	72_V	0.566	1.00
19_A	63_L	0.564	1.00
18_G	130_L	0.563	1.00
187_S	191_I	0.563	1.00
80_Y	108_M	0.562	1.00
318_A	326_A	0.560	1.00
63_L	114_L	0.560	1.00
350_D	353_Y	0.559	1.00
249_I	260_V	0.558	1.00
163_G	175_A	0.557	1.00
183_Q	271_T	0.555	1.00
165_D	285_L	0.555	1.00
159_K	319_R	0.553	1.00
6_T	156_I	0.553	1.00
16_V	162_I	0.552	1.00
284_A	331_L	0.551	1.00
313_D	317_N	0.550	1.00
306_R	310_A	0.549	1.00
62_L	65_G	0.549	1.00
145_L	148_L	0.547	1.00
242_M	245_L	0.547	1.00
77_C	80_Y	0.546	1.00
183_Q	187_S	0.544	1.00
184_Y	190_L	0.542	1.00
173_Q	178_G	0.542	1.00
160_L	327_S	0.542	1.00
30_A	159_K	0.540	1.00
239_N	242_M	0.539	1.00
23_G	308_V	0.539	1.00
136_L	150_L	0.539	1.00
268_F	273_R	0.538	1.00
84_E	94_V	0.537	1.00
140_H	143_D	0.537	1.00
20_L	315_L	0.536	1.00
201_D	206_Q	0.536	1.00
159_K	282_G	0.533	1.00
221_N	225_L	0.532	1.00
91_A	96_D	0.530	1.00
334_Y	338_R	0.530	1.00
187_S	190_L	0.527	1.00
57_A	61_S	0.526	1.00
291_H	338_R	0.526	1.00
72_V	107_Y	0.526	1.00
61_S	65_G	0.525	1.00
256_R	260_V	0.524	1.00
186_Q	296_L	0.524	1.00
194_Q	198_D	0.524	1.00
55_I	59_S	0.523	1.00
240_M	248_E	0.522	1.00
186_Q	189_M	0.521	1.00
177_I	181_A	0.521	1.00
73_Q	79_P	0.520	1.00
183_Q	189_M	0.519	1.00
29_F	320_S	0.518	1.00
238_Q	241_N	0.517	1.00
229_D	233_R	0.516	1.00
93_V	96_D	0.516	1.00
85_T	88_W	0.514	1.00
161_V	171_V	0.514	1.00
201_D	204_W	0.514	1.00
13_G	40_A	0.513	1.00
39_P	47_Q	0.513	1.00
257_L	262_P	0.512	1.00
329_P	332_K	0.512	1.00
238_Q	242_M	0.512	1.00
36_H	168_N	0.511	1.00
288_D	304_G	0.511	1.00
212_P	216_L	0.510	1.00
240_M	243_A	0.509	1.00
177_I	180_H	0.509	1.00
148_L	156_I	0.509	1.00
202_S	206_Q	0.509	1.00
20_L	164_A	0.508	1.00
123_E	132_V	0.508	1.00
63_L	72_V	0.507	1.00
344_I	348_G	0.507	1.00
181_A	273_R	0.506	1.00
40_A	116_Q	0.506	1.00
250_A	261_T	0.504	1.00
27_H	313_D	0.504	1.00
192_S	222_W	0.504	1.00
224_S	229_D	0.503	1.00
213_R	217_P	0.502	1.00
20_L	23_G	0.501	1.00
168_N	173_Q	0.501	1.00
310_A	334_Y	0.500	1.00

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
4n9xA	5	0.9258	100	0.246	Contact Map
2qa1A	2	0.9361	100	0.262	Contact Map
2qa2A	2	0.9437	100	0.266	Contact Map
4k5sA	2	0.9463	100	0.272	Contact Map
4k2xA	2	0.9335	100	0.299	Contact Map
2x3nA	1	0.9003	100	0.305	Contact Map
4k22A	4	0.9028	100	0.305	Contact Map
1pn0A	3	0.954	100	0.305	Contact Map
1k0iA	2	0.9591	100	0.312	Contact Map
2dkhA	2	0.9003	100	0.319	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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