YDJG - ECOLI - GREMLIN Contacts

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YDJG - Uncharacterized oxidoreductase YdjG

UniProt:	P77256	Sequences: MKKIPLGTTDITLSRMGLGTWAIGGGPAWNGDLDRQICIDTILEAHRCGINLIDTAPGYNFGNSEVIVGQALKKLPREQVVVETKCGIVWERKGSLFNKVGDRQLYKNLSPESIREEVAASLQRLGIDYIDIYMTHWQSVPPFFTPIAETVAVLNELKSEGKIRAIGAANVDADHIREYLQYGELDIIQAKYSILDRAMENELLPLCRDNGIVVQVYSPLEQGLLTGTITRDYVPGGARANKVWFQRENMLKVIDMLEQWQPLCARYQCTIPTLALAWILKQSDLISILSGATAPEQVRENVAALNINLSDADATLMREMAEALER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13483
Length:	326 (271)
Sequences:	31681 (19661)
Seq/√Len:	1194.3

ECOLI - YDJG YAJO TAS GPR YDHF YEAE YDBC DKGA DKGB
BACSU - GS69 IOLS YCCK YRPG YQKF YCSN YTBE GR
HALSA - Q9HPH9 Q9HQU7 Q9HNN3 Q9HSE6 Q9HS02 Q9HQT1
SULSO - Q97UG6 Q97ZZ1 Q97UJ7 Q97UV9 Q97V56 Q97U17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_E	299_R	3.209	1.00
119_A	162_K	2.917	1.00
35_R	70_Q	2.882	1.00
267_Y	313_D	2.818	1.00
73_K	126_G	2.782	1.00
310_S	313_D	2.483	1.00
115_R	156_E	2.417	1.00
39_I	74_K	2.415	1.00
118_V	157_L	2.412	1.00
5_P	12_T	2.369	1.00
44_E	48_C	2.361	1.00
115_R	160_E	2.321	1.00
266_R	316_L	2.212	1.00
155_N	159_S	2.147	1.00
281_K	314_A	2.090	1.00
261_Q	265_A	2.038	1.00
129_Y	164_R	2.032	1.00
39_I	70_Q	2.028	1.00
206_L	210_N	1.981	1.00
266_R	313_D	1.979	1.00
120_A	124_R	1.963	1.00
44_E	295_P	1.961	1.00
295_P	299_R	1.958	1.00
156_E	160_E	1.953	1.00
207_C	214_V	1.897	1.00
76_P	79_Q	1.883	1.00
17_G	52_L	1.874	1.00
262_P	316_L	1.862	1.00
311_D	315_T	1.856	1.00
111_P	156_E	1.828	1.00
48_C	299_R	1.811	1.00
282_Q	318_R	1.710	1.00
134_M	187_I	1.698	1.00
259_Q	262_P	1.696	1.00
156_E	159_S	1.686	1.00
269_C	307_I	1.668	1.00
66_V	124_R	1.667	1.00
39_I	43_L	1.660	1.00
177_R	181_Q	1.659	1.00
111_P	115_R	1.650	1.00
177_R	206_L	1.650	1.00
84_T	130_I	1.642	1.00
86_C	133_Y	1.637	1.00
48_C	302_V	1.627	1.00
303_A	306_N	1.625	1.00
270_T	300_E	1.622	1.00
82_V	127_I	1.620	1.00
45_A	50_I	1.602	1.00
153_V	156_E	1.594	1.00
84_T	121_S	1.593	1.00
118_V	133_Y	1.590	1.00
44_E	47_R	1.589	1.00
277_A	307_I	1.587	1.00
43_L	74_K	1.578	1.00
213_V	287_S	1.577	1.00
315_T	319_E	1.574	1.00
34_D	37_I	1.573	1.00
115_R	119_A	1.573	1.00
86_C	114_I	1.551	1.00
39_I	71_A	1.531	1.00
20_T	53_I	1.508	1.00
63_N	66_V	1.497	1.00
83_E	134_M	1.496	1.00
11_I	165_A	1.491	1.00
35_R	39_I	1.489	1.00
116_E	120_A	1.486	1.00
202_E	205_P	1.462	1.00
57_P	117_E	1.436	1.00
172_D	175_H	1.435	1.00
134_M	215_Q	1.433	1.00
46_H	80_V	1.419	1.00
37_I	40_D	1.417	1.00
269_C	273_T	1.417	1.00
180_L	210_N	1.411	1.00
119_A	123_Q	1.402	1.00
42_I	71_A	1.400	1.00
205_P	209_D	1.357	1.00
130_I	163_I	1.349	1.00
208_R	283_S	1.348	1.00
111_P	152_A	1.326	1.00
40_D	44_E	1.314	1.00
115_R	153_V	1.313	1.00
299_R	303_A	1.311	1.00
316_L	319_E	1.310	1.00
269_C	274_L	1.308	1.00
180_L	206_L	1.298	1.00
11_I	81_V	1.288	1.00
277_A	281_K	1.284	1.00
190_A	214_V	1.280	1.00
43_L	47_R	1.279	1.00
173_A	206_L	1.276	1.00
157_L	163_I	1.276	1.00
120_A	123_Q	1.276	1.00
259_Q	316_L	1.263	1.00
262_P	266_R	1.250	1.00
163_I	166_I	1.238	1.00
125_L	130_I	1.235	1.00
148_A	182_Y	1.234	1.00
165_A	186_D	1.232	1.00
111_P	153_V	1.229	1.00
70_Q	126_G	1.224	1.00
53_I	68_V	1.219	1.00
69_G	126_G	1.207	1.00
292_A	297_Q	1.205	1.00
204_L	208_R	1.203	1.00
81_V	132_I	1.181	1.00
270_T	273_T	1.179	1.00
36_Q	40_D	1.176	1.00
66_V	70_Q	1.174	1.00
65_E	121_S	1.170	1.00
292_A	298_V	1.170	1.00
261_Q	271_I	1.168	1.00
77_R	127_I	1.167	1.00
138_Q	175_H	1.166	1.00
43_L	75_L	1.164	1.00
177_R	209_D	1.160	1.00
113_S	116_E	1.135	1.00
263_L	274_L	1.128	1.00
177_R	210_N	1.128	1.00
20_T	68_V	1.125	1.00
132_I	187_I	1.121	1.00
296_E	299_R	1.118	1.00
110_S	113_S	1.114	1.00
52_L	215_Q	1.113	1.00
112_E	116_E	1.112	1.00
155_N	158_K	1.111	1.00
118_V	130_I	1.110	1.00
191_K	196_D	1.108	1.00
279_I	288_I	1.103	1.00
158_K	186_D	1.102	1.00
52_L	83_E	1.100	1.00
208_R	284_D	1.093	1.00
192_Y	282_Q	1.090	1.00
77_R	129_Y	1.085	1.00
40_D	295_P	1.082	1.00
194_I	317_M	1.082	1.00
260_W	271_I	1.081	1.00
119_A	160_E	1.077	1.00
154_L	166_I	1.076	1.00
51_N	81_V	1.067	1.00
135_T	154_L	1.059	1.00
195_L	257_L	1.056	1.00
173_A	177_R	1.055	1.00
258_E	261_Q	1.054	1.00
9_T	165_A	1.052	1.00
262_P	265_A	1.049	1.00
41_T	298_V	1.048	1.00
155_N	184_E	1.037	1.00
258_E	262_P	1.035	1.00
273_T	303_A	1.031	1.00
149_E	152_A	1.024	1.00
8_T	186_D	1.021	1.00
109_L	135_T	1.011	1.00
178_E	182_Y	1.010	1.00
5_P	10_D	1.006	1.00
157_L	162_K	1.001	1.00
43_L	71_A	1.000	1.00
199_M	214_V	0.996	1.00
159_S	184_E	0.995	1.00
72_L	80_V	0.989	1.00
187_I	215_Q	0.977	1.00
273_T	300_E	0.976	1.00
148_A	178_E	0.976	1.00
15_R	280_L	0.974	1.00
14_S	51_N	0.961	1.00
131_D	164_R	0.959	1.00
280_L	304_A	0.954	1.00
168_A	185_L	0.954	1.00
215_Q	287_S	0.952	1.00
201_N	205_P	0.951	1.00
9_T	186_D	0.946	1.00
152_A	156_E	0.942	1.00
157_L	160_E	0.933	1.00
70_Q	74_K	0.928	1.00
115_R	118_V	0.923	1.00
205_P	208_R	0.923	1.00
14_S	50_I	0.923	1.00
40_D	43_L	0.923	1.00
194_I	275_A	0.916	1.00
65_E	124_R	0.911	1.00
300_E	303_A	0.908	1.00
15_R	305_L	0.907	1.00
153_V	157_L	0.907	1.00
168_A	176_I	0.898	1.00
294_A	297_Q	0.898	1.00
111_P	149_E	0.897	1.00
298_V	302_V	0.897	1.00
281_K	308_N	0.894	1.00
152_A	155_N	0.889	1.00
42_I	53_I	0.889	1.00
176_I	212_I	0.888	1.00
115_R	157_L	0.884	1.00
116_E	119_A	0.883	1.00
230_T	261_Q	0.877	1.00
312_A	316_L	0.870	1.00
296_E	300_E	0.868	1.00
166_I	185_L	0.865	1.00
312_A	315_T	0.863	1.00
46_H	76_P	0.859	1.00
89_V	108_N	0.856	1.00
315_T	318_R	0.854	1.00
206_L	209_D	0.853	1.00
208_R	285_L	0.852	1.00
197_R	200_E	0.849	1.00
178_E	181_Q	0.849	1.00
57_P	113_S	0.844	1.00
282_Q	314_A	0.843	1.00
66_V	123_Q	0.843	1.00
155_N	183_G	0.839	1.00
83_E	215_Q	0.836	1.00
18_L	45_A	0.831	1.00
9_T	158_K	0.829	1.00
188_I	207_C	0.829	1.00
263_L	267_Y	0.819	1.00
197_R	318_R	0.817	1.00
83_E	132_I	0.813	1.00
276_L	304_A	0.809	1.00
35_R	67_I	0.807	1.00
155_N	166_I	0.804	1.00
204_L	214_V	0.799	1.00
57_P	124_R	0.789	1.00
266_R	310_S	0.784	1.00
259_Q	320_M	0.784	1.00
173_A	203_L	0.780	1.00
267_Y	310_S	0.778	1.00
20_T	64_S	0.771	1.00
170_N	217_Y	0.771	1.00
57_P	120_A	0.767	1.00
173_A	202_E	0.766	1.00
230_T	258_E	0.765	1.00
275_A	279_I	0.764	1.00
55_T	68_V	0.763	1.00
50_I	302_V	0.758	1.00
38_C	67_I	0.756	1.00
46_H	75_L	0.755	1.00
122_L	162_K	0.752	1.00
251_L	255_D	0.749	1.00
146_P	149_E	0.748	1.00
281_K	311_D	0.746	1.00
36_Q	39_I	0.744	1.00
48_C	303_A	0.742	1.00
44_E	298_V	0.737	1.00
137_W	170_N	0.736	1.00
278_W	318_R	0.735	1.00
219_P	290_S	0.734	1.00
192_Y	204_L	0.733	1.00
277_A	304_A	0.731	1.00
122_L	127_I	0.730	1.00
108_N	113_S	0.728	1.00
197_R	201_N	0.727	1.00
203_L	207_C	0.726	1.00
35_R	63_N	0.725	1.00
309_L	314_A	0.725	1.00
118_V	162_K	0.725	1.00
151_V	179_Y	0.723	1.00
117_E	120_A	0.723	1.00
46_H	53_I	0.716	1.00
114_I	157_L	0.716	1.00
17_G	290_S	0.713	1.00
16_M	280_L	0.713	1.00
168_A	171_V	0.708	1.00
43_L	76_P	0.708	1.00
151_V	183_G	0.704	1.00
269_C	303_A	0.704	1.00
84_T	133_Y	0.699	1.00
265_A	268_Q	0.698	1.00
216_V	219_P	0.695	1.00
272_P	300_E	0.693	1.00
78_E	129_Y	0.692	1.00
114_I	150_T	0.686	1.00
151_V	185_L	0.683	1.00
213_V	286_I	0.682	1.00
293_T	297_Q	0.682	1.00
151_V	166_I	0.680	1.00
109_L	150_T	0.680	1.00
263_L	313_D	0.678	1.00
216_V	288_I	0.677	1.00
255_D	258_E	0.675	1.00
207_C	212_I	0.672	1.00
192_Y	279_I	0.671	1.00
11_I	164_R	0.666	1.00
17_G	287_S	0.662	1.00
204_L	282_Q	0.662	1.00
134_M	167_G	0.662	1.00
41_T	295_P	0.659	1.00
175_H	178_E	0.659	1.00
254_I	258_E	0.659	1.00
18_L	23_I	0.659	1.00
22_A	222_Q	0.655	1.00
260_W	275_A	0.654	1.00
260_W	317_M	0.652	1.00
279_I	286_I	0.650	1.00
154_L	158_K	0.649	1.00
13_L	287_S	0.647	1.00
269_C	306_N	0.645	1.00
177_R	180_L	0.645	1.00
145_T	149_E	0.644	1.00
71_A	75_L	0.643	1.00
267_Y	274_L	0.642	1.00
121_S	133_Y	0.637	1.00
147_I	182_Y	0.637	1.00
274_L	309_L	0.636	1.00
150_T	153_V	0.636	1.00
297_Q	300_E	0.635	1.00
37_I	295_P	0.635	1.00
51_N	79_Q	0.631	1.00
168_A	188_I	0.630	1.00
58_G	87_G	0.629	1.00
114_I	153_V	0.629	1.00
48_C	298_V	0.629	1.00
219_P	279_I	0.627	1.00
46_H	79_Q	0.626	1.00
158_K	165_A	0.625	1.00
257_L	261_Q	0.624	1.00
8_T	211_G	0.623	1.00
192_Y	214_V	0.621	1.00
274_L	307_I	0.620	1.00
63_N	67_I	0.618	1.00
42_I	68_V	0.617	1.00
23_I	41_T	0.616	1.00
313_D	316_L	0.612	1.00
23_I	38_C	0.611	1.00
122_L	130_I	0.610	1.00
115_R	162_K	0.610	1.00
42_I	46_H	0.607	1.00
41_T	292_A	0.606	1.00
47_R	295_P	0.605	1.00
21_W	218_S	0.604	1.00
76_P	80_V	0.600	1.00
192_Y	286_I	0.600	1.00
264_C	274_L	0.598	1.00
86_C	109_L	0.597	1.00
130_I	133_Y	0.596	1.00
273_T	307_I	0.594	1.00
269_C	277_A	0.593	1.00
282_Q	286_I	0.593	1.00
180_L	183_G	0.590	1.00
147_I	150_T	0.589	1.00
280_L	288_I	0.588	1.00
263_L	316_L	0.588	1.00
274_L	313_D	0.586	1.00
274_L	317_M	0.581	1.00
264_C	267_Y	0.581	1.00
218_S	222_Q	0.580	1.00
263_L	320_M	0.579	1.00
122_L	129_Y	0.578	1.00
158_K	163_I	0.578	1.00
118_V	122_L	0.577	1.00
110_S	150_T	0.575	1.00
46_H	51_N	0.575	1.00
54_D	189_Q	0.574	1.00
25_G	67_I	0.574	1.00
180_L	184_E	0.571	1.00
255_D	259_Q	0.567	1.00
309_L	313_D	0.566	1.00
86_C	117_E	0.566	1.00
179_Y	185_L	0.565	1.00
139_S	145_T	0.563	1.00
180_L	212_I	0.561	1.00
168_A	179_Y	0.557	1.00
199_M	204_L	0.556	1.00
135_T	150_T	0.556	1.00
195_L	224_L	0.554	1.00
264_C	271_I	0.553	1.00
192_Y	200_E	0.551	1.00
216_V	285_L	0.547	1.00
254_I	257_L	0.546	1.00
46_H	71_A	0.546	1.00
53_I	72_L	0.546	1.00
13_L	52_L	0.545	1.00
138_Q	171_V	0.544	1.00
118_V	153_V	0.544	1.00
158_K	166_I	0.541	1.00
260_W	264_C	0.541	1.00
148_A	152_A	0.538	1.00
133_Y	163_I	0.537	1.00
17_G	289_L	0.536	1.00
57_P	90_W	0.536	1.00
55_T	64_S	0.535	1.00
24_G	64_S	0.535	1.00
6_L	213_V	0.530	1.00
250_M	253_V	0.529	1.00
18_L	41_T	0.529	1.00
277_A	308_N	0.528	1.00
88_I	109_L	0.528	1.00
174_D	177_R	0.527	1.00
122_L	128_D	0.526	1.00
216_V	279_I	0.526	1.00
224_L	257_L	0.526	1.00
66_V	126_G	0.525	1.00
57_P	87_G	0.524	1.00
139_S	144_F	0.524	1.00
133_Y	154_L	0.523	1.00
111_P	114_I	0.519	1.00
190_A	203_L	0.518	1.00
52_L	81_V	0.518	1.00
70_Q	73_K	0.517	1.00
192_Y	197_R	0.516	1.00
85_K	136_H	0.515	1.00
276_L	301_N	0.514	1.00
147_I	175_H	0.512	1.00
68_V	71_A	0.507	1.00
72_L	76_P	0.505	1.00
267_Y	307_I	0.505	1.00
16_M	305_L	0.502	1.00
69_G	73_K	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
1pyfA	1	0.9479	100	0.086	Contact Map
1pz1A	1	0.954	100	0.09	Contact Map
3n2tA	1	0.9632	100	0.102	Contact Map
4xk2A	5	0.8896	100	0.105	Contact Map
3v0sA	1	0.8313	100	0.105	Contact Map
1lqaA	2	0.9632	100	0.108	Contact Map
3erpA	6	0.8834	100	0.123	Contact Map
3eauA	3	0.9356	100	0.125	Contact Map
3lutA	3	0.9325	100	0.126	Contact Map
3n6qA	5	0.8896	100	0.127	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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