UBIA - ECOLI - GREMLIN Contacts

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UBIA - 4-hydroxybenzoate octaprenyltransferase

UniProt:	P0AGK1	Sequences: MEWSLTQNKLLAFHRLMRTDKPIGALLLLWPTLWALWVATPGVPQLWILAVFVAGVWLMRAAGCVVNDYADRKFDGHVKRTANRPLPSGAVTEKEARALFVVLVLISFLLVLTLNTMTILLSIAALALAWVYPFMKRYTHLPQVVLGAAFGWSIPMAFAAVSESVPLSCWLMFLANILWAVAYDTQYAMVDRDDDVKIGIKSTAILFGQYDKLIIGILQIGVLALMAIIGELNGLGWGYYWSILVAGALFVYQQKLIANREREACFKAFMNNNYVGLVLFLGLAMSYWHF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11370
Length:	290 (274)
Sequences:	6353 (4280)
Seq/√Len:	258.6

ECOLI - UBIA CYOE MENA
BACSU - COXX1 COXX2 MENA
HALSA - COXX DGGGP LYEL Q9HQN6
SULSO - Q980Z2 COXX DGGGP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_R	93_E	4.621	1.00
69_Y	93_E	4.303	1.00
15_R	90_A	3.647	1.00
69_Y	97_R	3.447	1.00
62_A	104_V	3.155	1.00
79_K	82_A	3.090	1.00
92_T	95_E	3.004	1.00
115_N	118_T	2.713	1.00
230_G	239_Y	2.687	1.00
74_F	200_I	2.686	1.00
116_T	120_L	2.494	1.00
118_T	159_A	2.479	1.00
65_V	103_L	2.386	1.00
76_G	87_P	2.374	1.00
210_Y	214_I	2.336	1.00
242_S	282_G	2.294	1.00
25_A	57_W	2.263	1.00
193_D	196_V	2.229	1.00
252_Y	256_L	2.204	1.00
51_V	113_T	2.176	1.00
51_V	110_L	2.119	1.00
192_R	196_V	2.033	1.00
94_K	98_A	2.031	1.00
59_M	107_S	2.011	1.00
236_G	286_S	1.989	1.00
33_L	53_V	1.973	1.00
16_L	95_E	1.909	1.00
223_L	247_G	1.858	1.00
69_Y	96_A	1.824	1.00
196_V	205_I	1.748	1.00
65_V	99_L	1.745	1.00
70_A	134_F	1.742	1.00
77_H	198_I	1.732	1.00
178_L	221_G	1.707	1.00
117_M	159_A	1.699	1.00
112_L	119_I	1.671	1.00
148_A	173_F	1.669	1.00
91_V	96_A	1.647	1.00
135_M	145_V	1.630	1.00
98_A	102_V	1.608	1.00
261_E	264_A	1.604	1.00
104_V	126_L	1.597	1.00
131_V	145_V	1.595	1.00
135_M	138_Y	1.588	1.00
192_R	209_Q	1.568	1.00
86_L	96_A	1.535	1.00
58_L	106_I	1.532	1.00
248_A	252_Y	1.530	1.00
72_R	76_G	1.516	1.00
211_D	215_I	1.511	1.00
71_D	137_R	1.506	1.00
273_N	277_L	1.505	1.00
61_A	103_L	1.491	1.00
142_P	202_S	1.462	1.00
65_V	100_F	1.458	1.00
267_K	270_M	1.454	1.00
189_M	211_D	1.447	1.00
214_I	218_L	1.427	1.00
175_A	226_M	1.426	1.00
128_L	149_A	1.422	1.00
192_R	205_I	1.421	1.00
166_P	169_C	1.414	1.00
222_V	226_M	1.387	1.00
120_L	124_A	1.377	1.00
245_V	249_L	1.369	1.00
91_V	99_L	1.364	1.00
65_V	91_V	1.354	1.00
50_A	54_A	1.343	1.00
127_A	131_V	1.342	1.00
282_G	286_S	1.333	1.00
264_A	268_A	1.329	1.00
59_M	122_S	1.328	1.00
29_L	33_L	1.321	1.00
165_V	169_C	1.321	1.00
14_H	19_T	1.320	1.00
246_A	279_L	1.313	1.00
182_A	219_Q	1.310	1.00
253_Q	256_L	1.297	1.00
249_L	271_N	1.291	1.00
71_D	74_F	1.288	1.00
17_M	99_L	1.283	1.00
230_G	240_Y	1.271	1.00
45_Q	48_I	1.261	1.00
155_P	173_F	1.252	1.00
86_L	91_V	1.248	1.00
272_N	276_G	1.243	1.00
74_F	137_R	1.239	1.00
274_Y	278_V	1.238	1.00
14_H	18_R	1.224	1.00
36_L	49_L	1.221	1.00
165_V	170_W	1.220	1.00
249_L	252_Y	1.214	1.00
266_F	270_M	1.199	1.00
29_L	53_V	1.199	1.00
47_W	51_V	1.191	1.00
170_W	174_L	1.186	1.00
58_L	107_S	1.173	1.00
227_A	230_G	1.170	1.00
93_E	97_R	1.158	1.00
111_V	122_S	1.150	1.00
91_V	95_E	1.148	1.00
167_L	170_W	1.142	1.00
221_G	225_L	1.137	1.00
108_F	123_I	1.137	1.00
262_R	265_C	1.137	1.00
271_N	275_V	1.134	1.00
251_V	255_K	1.129	1.00
20_D	61_A	1.122	1.00
66_V	100_F	1.120	1.00
223_L	227_A	1.118	1.00
55_G	111_V	1.118	1.00
231_E	240_Y	1.117	1.00
109_L	113_T	1.116	1.00
270_M	273_N	1.116	1.00
274_Y	277_L	1.115	1.00
151_G	180_A	1.113	1.00
72_R	86_L	1.104	1.00
32_T	56_V	1.099	1.00
151_G	176_N	1.097	1.00
39_A	161_V	1.097	1.00
97_R	101_V	1.096	1.00
51_V	114_L	1.091	1.00
32_T	52_F	1.091	1.00
151_G	177_I	1.087	1.00
58_L	103_L	1.078	1.00
101_V	105_L	1.078	1.00
211_D	214_I	1.077	1.00
118_T	156_M	1.074	1.00
246_A	275_V	1.072	1.00
71_D	133_P	1.070	1.00
69_Y	86_L	1.067	1.00
39_A	158_F	1.064	1.00
188_A	204_A	1.052	1.00
115_N	121_L	1.051	1.00
190_V	266_F	1.043	1.00
203_T	207_F	1.034	1.00
272_N	277_L	1.034	1.00
36_L	52_F	1.021	1.00
69_Y	100_F	1.018	1.00
253_Q	271_N	1.000	1.00
220_I	224_A	0.998	1.00
78_V	194_D	0.995	1.00
128_L	148_A	0.989	1.00
189_M	209_Q	0.986	1.00
176_N	180_A	0.979	1.00
178_L	218_L	0.974	1.00
140_H	201_K	0.972	1.00
256_L	264_A	0.970	1.00
171_L	232_L	0.969	1.00
263_E	267_K	0.967	1.00
227_A	243_I	0.961	1.00
79_K	193_D	0.959	1.00
70_A	133_P	0.956	1.00
210_Y	213_L	0.954	1.00
125_A	152_W	0.952	1.00
17_M	22_P	0.948	1.00
99_L	103_L	0.948	1.00
237_W	241_W	0.943	1.00
135_M	139_T	0.942	1.00
216_G	254_Q	0.941	1.00
38_V	158_F	0.940	1.00
65_V	96_A	0.940	1.00
227_A	231_E	0.939	1.00
252_Y	255_K	0.934	1.00
269_F	273_N	0.933	1.00
123_I	127_A	0.933	1.00
193_D	197_K	0.932	1.00
155_P	169_C	0.929	1.00
125_A	156_M	0.924	1.00
41_P	44_P	0.922	1.00
164_S	168_S	0.920	1.00
117_M	163_E	0.919	1.00
108_F	119_I	0.918	1.00
87_P	96_A	0.907	1.00
73_K	77_H	0.905	1.00
260_R	264_A	0.902	1.00
150_F	180_A	0.898	1.00
244_L	248_A	0.895	1.00
47_W	50_A	0.893	1.00
18_R	90_A	0.890	1.00
269_F	272_N	0.888	1.00
201_K	206_L	0.884	1.00
158_F	169_C	0.884	1.00
122_S	156_M	0.883	1.00
109_L	112_L	0.882	1.00
151_G	157_A	0.881	1.00
152_W	156_M	0.880	1.00
236_G	239_Y	0.878	1.00
18_R	85_P	0.875	1.00
250_F	253_Q	0.873	1.00
213_L	216_G	0.869	1.00
42_G	45_Q	0.867	1.00
26_L	273_N	0.867	1.00
74_F	198_I	0.865	1.00
54_A	110_L	0.864	1.00
117_M	121_L	0.856	1.00
117_M	120_L	0.856	1.00
207_F	211_D	0.855	1.00
40_T	161_V	0.854	0.99
228_I	232_L	0.854	0.99
66_V	101_V	0.847	0.99
32_T	153_S	0.839	0.99
112_L	116_T	0.836	0.99
108_F	112_L	0.833	0.99
113_T	116_T	0.833	0.99
174_L	178_L	0.829	0.99
220_I	223_L	0.827	0.99
158_F	166_P	0.827	0.99
45_Q	161_V	0.822	0.99
184_D	187_Y	0.818	0.99
139_T	145_V	0.815	0.99
73_K	76_G	0.814	0.99
238_G	242_S	0.814	0.99
95_E	98_A	0.812	0.99
68_D	71_D	0.807	0.99
270_M	274_Y	0.805	0.99
36_L	161_V	0.804	0.99
191_D	195_D	0.799	0.99
37_W	284_A	0.799	0.99
40_T	44_P	0.788	0.99
23_I	27_L	0.787	0.99
105_L	109_L	0.786	0.99
147_G	181_V	0.785	0.99
36_L	40_T	0.785	0.99
271_N	274_Y	0.783	0.99
20_D	103_L	0.782	0.99
13_F	17_M	0.780	0.99
224_A	228_I	0.780	0.99
164_S	167_L	0.776	0.99
131_V	135_M	0.776	0.99
71_D	200_I	0.773	0.99
35_A	39_A	0.772	0.99
154_I	176_N	0.770	0.99
143_Q	185_T	0.769	0.99
239_Y	243_I	0.767	0.99
230_G	233_N	0.765	0.99
21_K	266_F	0.764	0.99
34_W	284_A	0.763	0.99
175_A	225_L	0.761	0.99
227_A	240_Y	0.759	0.99
186_Q	257_I	0.758	0.99
143_Q	184_D	0.756	0.99
146_L	183_Y	0.753	0.99
66_V	70_A	0.751	0.99
256_L	267_K	0.747	0.99
154_I	160_A	0.743	0.99
111_V	119_I	0.743	0.99
260_R	265_C	0.742	0.99
114_L	118_T	0.740	0.99
17_M	20_D	0.737	0.99
225_L	228_I	0.737	0.99
224_A	227_A	0.733	0.98
240_Y	244_L	0.731	0.98
275_V	279_L	0.731	0.98
166_P	170_W	0.728	0.98
175_A	222_V	0.727	0.98
143_Q	180_A	0.725	0.98
79_K	194_D	0.724	0.98
242_S	278_V	0.720	0.98
168_S	233_N	0.720	0.98
242_S	246_A	0.716	0.98
256_L	268_A	0.716	0.98
163_E	166_P	0.714	0.98
114_L	119_I	0.712	0.98
212_K	254_Q	0.712	0.98
48_I	114_L	0.708	0.98
158_F	162_S	0.707	0.98
139_T	203_T	0.706	0.98
250_F	254_Q	0.705	0.98
144_V	181_V	0.704	0.98
249_L	253_Q	0.704	0.98
182_A	222_V	0.703	0.98
116_T	119_I	0.703	0.98
61_A	99_L	0.702	0.98
37_W	280_F	0.702	0.98
238_G	285_M	0.701	0.98
69_Y	72_R	0.697	0.98
280_F	284_A	0.697	0.98
48_I	161_V	0.694	0.98
183_Y	187_Y	0.694	0.98
64_C	68_D	0.693	0.98
194_D	197_K	0.691	0.98
14_H	17_M	0.688	0.98
85_P	90_A	0.686	0.98
95_E	99_L	0.685	0.98
16_L	91_V	0.683	0.98
279_L	282_G	0.683	0.98
281_L	285_M	0.681	0.98
235_L	286_S	0.681	0.98
115_N	160_A	0.676	0.97
86_L	89_G	0.675	0.97
222_V	227_A	0.672	0.97
33_L	49_L	0.671	0.97
195_D	202_S	0.670	0.97
121_L	159_A	0.667	0.97
111_V	114_L	0.666	0.97
102_V	106_I	0.663	0.97
85_P	89_G	0.660	0.97
16_L	99_L	0.658	0.97
230_G	235_L	0.658	0.97
277_L	281_L	0.657	0.97
171_L	228_I	0.655	0.97
59_M	126_L	0.655	0.97
47_W	54_A	0.654	0.97
154_I	157_A	0.654	0.97
243_I	247_G	0.653	0.97
35_A	38_V	0.652	0.97
178_L	225_L	0.649	0.97
141_L	144_V	0.647	0.97
140_H	206_L	0.647	0.97
272_N	275_V	0.645	0.97
79_K	83_N	0.643	0.96
102_V	109_L	0.642	0.96
268_A	273_N	0.641	0.96
22_P	25_A	0.640	0.96
150_F	183_Y	0.639	0.96
251_V	254_Q	0.637	0.96
185_T	203_T	0.636	0.96
128_L	145_V	0.635	0.96
118_T	122_S	0.631	0.96
78_V	195_D	0.630	0.96
243_I	246_A	0.630	0.96
229_I	233_N	0.629	0.96
146_L	187_Y	0.619	0.96
27_L	276_G	0.617	0.96
237_W	240_Y	0.616	0.96
100_F	104_V	0.614	0.95
212_K	216_G	0.613	0.95
242_S	247_G	0.613	0.95
243_I	282_G	0.612	0.95
252_Y	271_N	0.611	0.95
189_M	192_R	0.608	0.95
19_T	25_A	0.607	0.95
283_L	286_S	0.605	0.95
35_A	157_A	0.605	0.95
66_V	130_W	0.602	0.95
223_L	226_M	0.601	0.95
37_W	40_T	0.600	0.95
255_K	259_N	0.600	0.95
117_M	162_S	0.599	0.95
133_P	184_D	0.599	0.95
146_L	180_A	0.598	0.95
104_V	108_F	0.593	0.95
60_R	187_Y	0.590	0.94
217_I	221_G	0.590	0.94
73_K	93_E	0.588	0.94
207_F	214_I	0.584	0.94
60_R	64_C	0.584	0.94
255_K	258_A	0.583	0.94
55_G	110_L	0.581	0.94
110_L	113_T	0.580	0.94
74_F	77_H	0.580	0.94
279_L	283_L	0.576	0.94
171_L	225_L	0.575	0.94
185_T	212_K	0.575	0.94
184_D	188_A	0.574	0.94
241_W	245_V	0.573	0.93
249_L	275_V	0.573	0.93
214_I	258_A	0.572	0.93
254_Q	258_A	0.572	0.93
208_G	212_K	0.569	0.93
143_Q	181_V	0.564	0.93
52_F	160_A	0.562	0.93
193_D	262_R	0.561	0.93
111_V	156_M	0.558	0.93
146_L	184_D	0.558	0.93
231_E	234_G	0.558	0.93
249_L	256_L	0.557	0.93
236_G	240_Y	0.556	0.92
152_W	155_P	0.554	0.92
43_V	47_W	0.553	0.92
256_L	259_N	0.553	0.92
24_G	64_C	0.549	0.92
78_V	133_P	0.548	0.92
97_R	130_W	0.547	0.92
280_F	283_L	0.546	0.92
248_A	255_K	0.544	0.92
215_I	219_Q	0.541	0.91
97_R	100_F	0.541	0.91
245_V	248_A	0.535	0.91
19_T	57_W	0.533	0.91
38_V	229_I	0.533	0.91
203_T	218_L	0.531	0.91
141_L	206_L	0.531	0.91
24_G	184_D	0.529	0.90
258_A	261_E	0.529	0.90
78_V	183_Y	0.529	0.90
39_A	157_A	0.528	0.90
273_N	276_G	0.524	0.90
167_L	171_L	0.521	0.90
145_V	178_L	0.520	0.90
244_L	247_G	0.519	0.90
174_L	225_L	0.518	0.90
264_A	267_K	0.516	0.89
24_G	71_D	0.514	0.89
179_W	183_Y	0.513	0.89
187_Y	190_V	0.512	0.89
28_L	32_T	0.512	0.89
213_L	258_A	0.512	0.89
57_W	61_A	0.511	0.89
58_L	110_L	0.510	0.89
209_Q	213_L	0.510	0.89
242_S	286_S	0.509	0.89
154_I	158_F	0.507	0.89
263_E	270_M	0.505	0.88
216_G	268_A	0.504	0.88
210_Y	258_A	0.504	0.88
254_Q	257_I	0.503	0.88
32_T	36_L	0.502	0.88
115_N	163_E	0.502	0.88
127_A	148_A	0.500	0.88

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
4od4A	1	0.9172	100	0.239	Contact Map
4tq3A	1	0.9414	100	0.317	Contact Map
2xq2A	2	0.7724	32.7	0.946	Contact Map
1fftA	1	0	11.1	0.957	Contact Map
3ze3A	4	0.369	8.7	0.959	Contact Map
4xnjA	1	0.5862	7.6	0.96	Contact Map
3ixzA	1	0.6724	4.2	0.964	Contact Map
4uc1A	3	0.5241	3.4	0.966	Contact Map
2cfqA	1	0.8931	3	0.967	Contact Map
1a87A	1	0.2724	2.8	0.967	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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