YGBJ - ECOLI - GREMLIN Contacts

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YGBJ - Uncharacterized oxidoreductase YgbJ

UniProt:	Q46888	Sequences: MKTGSEFHVGIVGLGSMGMGAALSYVRAGLSTWGADLNSNACATLKEAGACGVSDNAATFAEKLDALLVLVVNAAQVKQVLFGETGVAQHLKPGTAVMVSSTIASADAQEIATALAGFDLEMLDAPVSGGAVKAANGEMTVMASGSDIAFERLAPVLEAVAGKVYRIGAEPGLGSTVKIIHQLLAGVHIAAGAEAMALAARAGIPLDVMYDVVTNAAGNSWMFENRMRHVVDGDYTPHSAVDIFVKDLGLVADTAKALHFPLPLASTALNMFTSASNAGYGKEDDSAVIKIFSGITLPGAKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13104
Length:	302 (279)
Sequences:	11465 (7432)
Seq/√Len:	444.9

ECOLI - YGBJ GARR SQUU GLXR 6PGD
BACSU - YKWC YFJR YQEC 6PGDH 6PGD
HALSA - Q9HMG5
SULSO - Q97XZ7 Q97ZE5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
154_A	158_E	3.657	1.00
78_K	110_E	3.391	1.00
147_D	151_E	3.378	1.00
33_W	54_S	3.017	1.00
8_H	31_S	2.943	1.00
46_K	53_V	2.863	1.00
121_E	149_A	2.860	1.00
121_E	152_R	2.711	1.00
23_L	48_A	2.685	1.00
242_D	282_K	2.336	1.00
55_D	59_T	2.253	1.00
43_A	47_E	2.237	1.00
151_E	154_A	2.224	1.00
42_C	53_V	2.149	1.00
115_L	120_L	2.145	1.00
10_G	60_F	2.072	1.00
96_A	153_L	2.024	1.00
219_N	224_E	2.008	1.00
205_P	208_V	1.981	1.00
56_N	59_T	1.965	1.00
19_M	44_T	1.939	1.00
88_A	115_L	1.891	1.00
30_L	159_A	1.889	1.00
147_D	166_R	1.867	1.00
58_A	62_E	1.836	1.00
112_A	171_P	1.832	1.00
106_A	257_A	1.815	1.00
69_V	97_V	1.811	1.00
121_E	146_S	1.804	1.00
8_H	33_W	1.800	1.00
24_S	27_R	1.800	1.00
31_S	51_C	1.786	1.00
26_V	50_A	1.777	1.00
254_T	257_A	1.775	1.00
28_A	159_A	1.772	1.00
38_N	41_A	1.732	1.00
92_K	95_T	1.709	1.00
40_N	43_A	1.696	1.00
146_S	149_A	1.694	1.00
116_A	146_S	1.687	1.00
33_W	63_K	1.679	1.00
113_T	117_G	1.679	1.00
199_A	209_M	1.646	1.00
60_F	64_L	1.623	1.00
70_L	100_S	1.621	1.00
141_V	160_V	1.619	1.00
34_G	50_A	1.611	1.00
81_L	97_V	1.603	1.00
39_S	43_A	1.602	1.00
123_L	145_G	1.587	1.00
96_A	149_A	1.585	1.00
114_A	117_G	1.576	1.00
242_D	276_S	1.569	1.00
280_Y	283_E	1.554	1.00
150_F	154_A	1.527	1.00
112_A	116_A	1.526	1.00
110_E	114_A	1.513	1.00
91_L	95_T	1.505	1.00
24_S	137_G	1.478	1.00
123_L	153_L	1.478	1.00
125_A	141_V	1.476	1.00
141_V	161_A	1.466	1.00
68_L	100_S	1.447	1.00
207_D	211_D	1.438	1.00
270_N	273_T	1.427	1.00
150_F	166_R	1.401	1.00
228_R	232_D	1.389	1.00
167_I	177_V	1.382	1.00
33_W	51_C	1.380	1.00
131_A	135_A	1.378	1.00
73_N	76_Q	1.377	1.00
58_A	90_H	1.377	1.00
241_V	275_A	1.375	1.00
179_I	250_L	1.374	1.00
187_V	191_A	1.371	1.00
43_A	46_K	1.370	1.00
132_V	136_N	1.354	1.00
266_S	270_N	1.340	1.00
74_A	107_D	1.336	1.00
65_D	92_K	1.310	1.00
96_A	152_R	1.304	1.00
108_A	122_M	1.295	1.00
214_T	224_E	1.294	1.00
27_R	48_A	1.283	1.00
70_L	127_V	1.278	1.00
138_E	162_G	1.276	1.00
39_S	55_D	1.274	1.00
115_L	122_M	1.274	1.00
123_L	150_F	1.251	1.00
200_A	206_L	1.251	1.00
269_L	273_T	1.250	1.00
86_G	89_Q	1.249	1.00
98_M	153_L	1.244	1.00
283_E	290_K	1.242	1.00
23_L	135_A	1.234	1.00
27_R	135_A	1.233	1.00
242_D	281_G	1.229	1.00
267_T	270_N	1.224	1.00
20_G	135_A	1.222	1.00
75_A	79_Q	1.218	1.00
10_G	64_L	1.213	1.00
57_A	90_H	1.211	1.00
245_V	276_S	1.210	1.00
45_L	50_A	1.209	1.00
66_A	96_A	1.186	1.00
153_L	157_L	1.181	1.00
256_K	266_S	1.179	1.00
59_T	62_E	1.178	1.00
146_S	169_A	1.174	1.00
202_A	258_L	1.164	1.00
61_A	90_H	1.164	1.00
253_D	257_A	1.160	1.00
186_G	248_L	1.155	1.00
22_A	32_T	1.151	1.00
100_S	141_V	1.148	1.00
186_G	244_F	1.148	1.00
197_A	201_R	1.147	1.00
78_K	114_A	1.146	1.00
44_T	47_E	1.145	1.00
88_A	118_F	1.145	1.00
255_A	262_L	1.144	1.00
66_A	156_V	1.141	1.00
11_I	21_A	1.126	1.00
89_Q	118_F	1.122	1.00
104_A	107_D	1.119	1.00
95_T	120_L	1.111	1.00
91_L	120_L	1.108	1.00
11_I	68_L	1.107	1.00
109_Q	176_T	1.105	1.00
97_V	115_L	1.102	1.00
8_H	65_D	1.099	1.00
71_V	80_V	1.095	1.00
109_Q	171_P	1.093	1.00
23_L	27_R	1.086	1.00
11_I	22_A	1.083	1.00
261_P	266_S	1.071	1.00
33_W	64_L	1.057	1.00
78_K	107_D	1.051	1.00
74_A	104_A	1.050	1.00
239_S	243_I	1.042	1.00
100_S	160_V	1.042	1.00
68_L	156_V	1.042	1.00
16_S	131_A	1.035	1.00
109_Q	113_T	1.030	1.00
143_A	150_F	1.029	1.00
169_A	173_L	1.027	1.00
252_A	266_S	1.025	1.00
166_R	169_A	1.022	1.00
113_T	116_A	1.017	1.00
59_T	63_K	0.993	1.00
245_V	273_T	0.990	1.00
112_A	146_S	0.987	1.00
253_D	256_K	0.985	1.00
114_A	118_F	0.984	1.00
36_D	41_A	0.984	1.00
249_G	269_L	0.981	1.00
158_E	164_V	0.975	1.00
184_L	195_A	0.972	1.00
26_V	49_G	0.967	1.00
85_T	89_Q	0.965	1.00
241_V	276_S	0.964	1.00
123_L	143_A	0.961	1.00
214_T	223_F	0.958	1.00
134_A	139_M	0.953	1.00
124_D	172_G	0.949	1.00
54_S	59_T	0.948	1.00
180_I	199_A	0.944	1.00
63_K	92_K	0.942	1.00
85_T	114_A	0.940	1.00
58_A	86_G	0.938	1.00
128_S	181_H	0.936	1.00
167_I	173_L	0.928	1.00
227_M	231_V	0.928	1.00
54_S	60_F	0.927	1.00
91_L	97_V	0.926	1.00
208_V	211_D	0.924	1.00
14_L	45_L	0.923	1.00
196_M	210_Y	0.921	1.00
77_V	103_I	0.917	1.00
68_L	98_M	0.917	1.00
187_V	264_L	0.916	1.00
76_Q	79_Q	0.913	1.00
180_I	195_A	0.911	1.00
273_T	276_S	0.910	1.00
44_T	48_A	0.907	1.00
37_L	76_Q	0.906	1.00
145_G	150_F	0.906	1.00
93_P	119_D	0.900	1.00
151_E	166_R	0.897	1.00
39_S	53_V	0.893	1.00
81_L	115_L	0.892	1.00
249_G	273_T	0.884	1.00
128_S	142_M	0.884	1.00
249_G	253_D	0.882	1.00
142_M	212_V	0.877	1.00
104_A	253_D	0.877	1.00
276_S	281_G	0.876	1.00
24_S	160_V	0.873	1.00
66_A	152_R	0.873	1.00
283_E	287_A	0.872	1.00
273_T	277_N	0.870	1.00
167_I	212_V	0.869	1.00
78_K	111_I	0.867	1.00
107_D	110_E	0.864	1.00
40_N	44_T	0.856	1.00
108_A	175_S	0.853	1.00
11_I	32_T	0.851	1.00
14_L	34_G	0.849	1.00
96_A	121_E	0.846	1.00
103_I	107_D	0.845	1.00
19_M	23_L	0.845	1.00
240_A	243_I	0.844	1.00
227_M	230_V	0.838	1.00
176_T	254_T	0.837	1.00
176_T	202_A	0.834	1.00
221_W	225_N	0.834	1.00
81_L	87_V	0.833	1.00
110_E	113_T	0.831	1.00
124_D	174_G	0.828	1.00
226_R	229_H	0.821	1.00
201_R	260_F	0.821	1.00
21_A	160_V	0.816	1.00
9_V	30_L	0.814	1.00
188_H	220_S	0.810	1.00
155_P	158_E	0.806	1.00
280_Y	290_K	0.806	1.00
67_L	87_V	0.804	1.00
98_M	125_A	0.799	1.00
210_Y	227_M	0.795	1.00
275_A	287_A	0.793	1.00
41_A	44_T	0.793	1.00
190_A	264_L	0.792	1.00
25_Y	68_L	0.791	1.00
177_V	204_I	0.787	1.00
149_A	152_R	0.783	1.00
26_V	48_A	0.781	1.00
226_R	230_V	0.781	1.00
214_T	219_N	0.779	1.00
236_T	283_E	0.777	1.00
207_D	232_D	0.773	1.00
188_H	192_G	0.770	1.00
264_L	268_A	0.769	1.00
69_V	77_V	0.769	1.00
21_A	139_M	0.766	1.00
106_A	109_Q	0.760	1.00
150_F	164_V	0.759	1.00
147_D	169_A	0.759	1.00
144_S	174_G	0.756	1.00
102_T	250_L	0.755	1.00
109_Q	172_G	0.755	1.00
72_V	76_Q	0.755	1.00
201_R	258_L	0.748	1.00
34_G	42_C	0.747	1.00
245_V	269_L	0.746	1.00
130_G	133_K	0.745	1.00
60_F	63_K	0.744	1.00
21_A	100_S	0.743	1.00
99_V	122_M	0.740	1.00
157_L	164_V	0.732	1.00
66_A	98_M	0.732	1.00
123_L	149_A	0.731	1.00
149_A	153_L	0.730	1.00
183_L	265_A	0.727	1.00
88_A	120_L	0.725	1.00
210_Y	214_T	0.725	1.00
199_A	204_I	0.722	1.00
207_D	231_V	0.721	1.00
184_L	192_G	0.721	1.00
33_W	60_F	0.720	1.00
192_G	223_F	0.718	1.00
37_L	41_A	0.717	1.00
183_L	251_V	0.714	1.00
69_V	81_L	0.712	1.00
252_A	269_L	0.707	1.00
274_S	278_A	0.706	1.00
193_A	288_V	0.705	1.00
240_A	282_K	0.704	1.00
71_V	76_Q	0.702	1.00
121_E	148_I	0.702	1.00
21_A	70_L	0.699	1.00
254_T	258_L	0.699	1.00
39_S	42_C	0.699	1.00
242_D	246_K	0.698	1.00
274_S	291_I	0.698	1.00
9_V	25_Y	0.698	1.00
111_I	122_M	0.698	1.00
25_Y	32_T	0.696	1.00
11_I	70_L	0.695	1.00
8_H	63_K	0.694	1.00
278_A	291_I	0.688	1.00
19_M	48_A	0.688	1.00
51_C	63_K	0.686	1.00
163_K	215_N	0.685	1.00
275_A	291_I	0.683	1.00
235_Y	290_K	0.681	1.00
30_L	156_V	0.677	1.00
9_V	156_V	0.676	1.00
241_V	287_A	0.675	1.00
88_A	114_A	0.673	1.00
12_V	35_A	0.671	1.00
144_S	166_R	0.670	1.00
148_I	151_E	0.666	1.00
210_Y	213_V	0.666	1.00
154_A	164_V	0.660	1.00
122_M	171_P	0.659	1.00
256_K	269_L	0.655	1.00
12_V	57_A	0.654	1.00
71_V	77_V	0.654	1.00
165_Y	212_V	0.649	1.00
180_I	198_L	0.647	0.99
243_I	246_K	0.647	0.99
43_A	53_V	0.644	0.99
274_S	277_N	0.642	0.99
221_W	224_E	0.639	0.99
64_L	67_L	0.639	0.99
184_L	188_H	0.639	0.99
26_V	32_T	0.637	0.99
270_N	277_N	0.637	0.99
204_I	209_M	0.634	0.99
184_L	191_A	0.634	0.99
57_A	61_A	0.633	0.99
107_D	111_I	0.632	0.99
176_T	204_I	0.631	0.99
42_C	46_K	0.630	0.99
103_I	175_S	0.628	0.99
275_A	280_Y	0.627	0.99
197_A	200_A	0.626	0.99
77_V	101_S	0.625	0.99
241_V	246_K	0.625	0.99
177_V	209_M	0.624	0.99
143_A	157_L	0.622	0.99
62_E	90_H	0.620	0.99
184_L	213_V	0.620	0.99
189_I	285_D	0.619	0.99
125_A	143_A	0.618	0.99
19_M	45_L	0.616	0.99
188_H	222_M	0.615	0.99
79_Q	85_T	0.612	0.99
87_V	91_L	0.612	0.99
229_H	234_D	0.610	0.99
271_M	274_S	0.610	0.99
163_K	211_D	0.610	0.99
67_L	91_L	0.610	0.99
104_A	250_L	0.609	0.99
179_I	251_V	0.608	0.99
77_V	107_D	0.606	0.99
157_L	161_A	0.606	0.99
75_A	78_K	0.606	0.99
22_A	34_G	0.603	0.99
61_A	64_L	0.600	0.99
270_N	274_S	0.599	0.99
36_D	39_S	0.598	0.99
103_I	108_A	0.597	0.99
154_A	166_R	0.597	0.99
54_S	63_K	0.596	0.99
198_L	262_L	0.596	0.99
287_A	290_K	0.590	0.99
240_A	246_K	0.590	0.99
17_M	21_A	0.589	0.99
15_G	72_V	0.587	0.99
20_G	131_A	0.583	0.99
93_P	118_F	0.583	0.99
193_A	230_V	0.582	0.99
133_K	138_E	0.581	0.99
58_A	89_Q	0.581	0.99
35_A	57_A	0.579	0.99
58_A	85_T	0.579	0.99
79_Q	86_G	0.577	0.99
237_P	240_A	0.576	0.99
12_V	60_F	0.574	0.99
125_A	157_L	0.573	0.99
210_Y	231_V	0.572	0.99
225_N	229_H	0.572	0.99
36_D	76_Q	0.569	0.99
66_A	153_L	0.566	0.99
77_V	99_V	0.566	0.99
187_V	268_A	0.562	0.99
143_A	164_V	0.561	0.99
92_K	120_L	0.558	0.99
249_G	256_K	0.555	0.98
252_A	256_K	0.555	0.98
20_G	137_G	0.552	0.98
23_L	26_V	0.552	0.98
108_A	171_P	0.549	0.98
77_V	111_I	0.549	0.98
133_K	136_N	0.543	0.98
80_V	86_G	0.543	0.98
147_D	150_F	0.543	0.98
14_L	22_A	0.540	0.98
8_H	64_L	0.538	0.98
234_D	237_P	0.534	0.98
69_V	99_V	0.534	0.98
197_A	260_F	0.533	0.98
261_P	274_S	0.530	0.98
242_D	245_V	0.526	0.98
156_V	159_A	0.526	0.98
181_H	216_A	0.524	0.98
105_S	176_T	0.523	0.98
183_L	198_L	0.522	0.98
106_A	110_E	0.522	0.98
51_C	54_S	0.521	0.98
206_L	231_V	0.521	0.98
213_V	218_G	0.521	0.98
276_S	279_G	0.517	0.98
222_M	226_R	0.517	0.98
57_A	60_F	0.517	0.98
81_L	111_I	0.516	0.98
62_E	92_K	0.516	0.98
36_D	42_C	0.510	0.97
67_L	95_T	0.510	0.97
264_L	267_T	0.509	0.97
245_V	249_G	0.507	0.97
50_A	53_V	0.507	0.97
173_L	176_T	0.502	0.97
81_L	88_A	0.501	0.97
10_G	33_W	0.501	0.97
99_V	108_A	0.500	0.97
98_M	157_L	0.500	0.97

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
3dojA	3	0.9669	100	0.368	Contact Map
1vpdA	1	0.9735	100	0.372	Contact Map
3pefA	5	0.9503	100	0.374	Contact Map
3obbA	4	0.9536	100	0.375	Contact Map
3pduA	4	0.9503	100	0.375	Contact Map
3ckyA	4	0.9768	100	0.377	Contact Map
3g0oA	3	0.9404	100	0.379	Contact Map
3zgyA	2	0.957	100	0.382	Contact Map
3ws7A	2	0.947	100	0.383	Contact Map
2uyyA	3	0.9603	100	0.385	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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