YAJO - ECOLI - GREMLIN Contacts

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YAJO - Uncharacterized oxidoreductase YajO

UniProt:	P77735	Sequences: MQYNPLGKTDLRVSRLCLGCMTFGEPDRGNHAWTLPEESSRPIIKRALEGGINFFDTANSYSDGSSEEIVGRALRDFARREDVVVATKVFHRVGDLPEGLSRAQILRSIDDSLRRLGMDYVDILQIHRWDYNTPIEETLEALNDVVKAGKARYIGASSMHASQFAQALELQKQHGWAQFVSMQDHYNLIYREEEREMLPLCYQEGVAVIPWSPLARGRLTRPWGETTARLVSDEVGKNLYKESDENDAQIAERLTGVSEELGATRAQVALAWLLSKPGIAAPIIGTSREEQLDELLNAVDITLKPEQIAELETPYKPHPVVGFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13611
Length:	324 (267)
Sequences:	32139 (19946)
Seq/√Len:	1220.7

ECOLI - YAJO YDJG TAS GPR YDHF YEAE YDBC DKGA DKGB
BACSU - GS69 YCCK IOLS YRPG YQKF YCSN YTBE GR
HALSA - Q9HPH9 Q9HNN3 Q9HQU7 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
46_R	293_D	3.201	1.00
110_D	150_K	3.030	1.00
37_E	72_R	2.965	1.00
261_L	307_Q	2.834	1.00
75_R	117_G	2.816	1.00
109_I	145_V	2.544	1.00
304_K	307_Q	2.516	1.00
106_L	144_D	2.427	1.00
41_R	76_D	2.412	1.00
106_L	148_A	2.394	1.00
46_R	50_G	2.374	1.00
260_E	310_E	2.222	1.00
143_N	147_K	2.071	1.00
275_S	308_I	2.048	1.00
41_R	72_R	2.041	1.00
260_E	307_Q	2.030	1.00
255_T	259_E	2.020	1.00
120_Y	152_R	1.978	1.00
111_D	115_R	1.971	1.00
144_D	148_A	1.970	1.00
200_L	204_E	1.936	1.00
305_P	309_A	1.910	1.00
79_R	82_D	1.894	1.00
289_E	293_D	1.892	1.00
201_C	208_V	1.887	1.00
256_G	310_E	1.881	1.00
17_C	54_F	1.869	1.00
125_Q	181_S	1.810	1.00
102_R	144_D	1.807	1.00
65_S	68_E	1.802	1.00
46_R	289_E	1.801	1.00
50_G	293_D	1.770	1.00
85_V	118_M	1.760	1.00
87_T	121_V	1.753	1.00
276_K	312_E	1.746	1.00
165_A	169_E	1.737	1.00
263_A	301_I	1.719	1.00
144_D	147_K	1.719	1.00
68_E	115_R	1.699	1.00
271_A	301_I	1.695	1.00
253_R	256_G	1.659	1.00
102_R	106_L	1.652	1.00
47_A	52_I	1.649	1.00
50_G	296_L	1.637	1.00
264_T	294_E	1.633	1.00
165_A	200_L	1.620	1.00
87_T	112_S	1.610	1.00
41_R	45_K	1.607	1.00
297_N	300_D	1.605	1.00
41_R	73_A	1.602	1.00
89_V	124_L	1.599	1.00
109_I	124_L	1.590	1.00
207_A	281_A	1.589	1.00
89_V	105_I	1.586	1.00
309_A	313_T	1.582	1.00
36_P	39_S	1.571	1.00
106_L	110_D	1.567	1.00
86_A	125_Q	1.562	1.00
141_A	144_D	1.555	1.00
143_N	177_A	1.553	1.00
45_K	76_D	1.538	1.00
46_R	49_E	1.534	1.00
20_C	55_F	1.516	1.00
59_N	108_S	1.497	1.00
11_L	153_Y	1.493	1.00
125_Q	209_I	1.471	1.00
196_E	199_P	1.443	1.00
107_R	111_D	1.443	1.00
121_V	151_A	1.436	1.00
44_I	73_A	1.421	1.00
263_A	267_Q	1.419	1.00
48_L	83_V	1.413	1.00
39_S	42_P	1.405	1.00
110_D	114_R	1.402	1.00
202_Y	277_P	1.392	1.00
160_H	163_Q	1.390	1.00
168_L	204_E	1.386	1.00
199_P	203_Q	1.383	1.00
146_V	177_A	1.371	1.00
37_E	41_R	1.368	1.00
293_D	297_N	1.333	1.00
11_L	84_V	1.322	1.00
45_K	49_E	1.320	1.00
184_D	208_V	1.317	1.00
102_R	140_E	1.317	1.00
168_L	200_L	1.303	1.00
271_A	275_S	1.299	1.00
106_L	141_A	1.297	1.00
145_V	151_A	1.295	1.00
310_E	313_T	1.282	1.00
263_A	268_V	1.282	1.00
151_A	154_I	1.281	1.00
153_Y	180_V	1.276	1.00
111_D	114_R	1.273	1.00
42_P	46_R	1.261	1.00
253_R	310_E	1.261	1.00
102_R	141_A	1.253	1.00
286_T	291_Q	1.245	1.00
136_E	170_L	1.228	1.00
161_A	200_L	1.222	1.00
55_F	70_V	1.221	1.00
116_L	121_V	1.218	1.00
257_V	268_V	1.216	1.00
84_V	123_I	1.213	1.00
264_T	267_Q	1.211	1.00
256_G	260_E	1.208	1.00
80_R	120_Y	1.206	1.00
67_E	112_S	1.201	1.00
109_I	121_V	1.196	1.00
286_T	292_L	1.188	1.00
80_R	118_M	1.185	1.00
72_R	117_G	1.183	1.00
71_G	117_G	1.183	1.00
165_A	203_Q	1.176	1.00
68_E	72_R	1.166	1.00
198_L	202_Y	1.163	1.00
123_I	181_S	1.161	1.00
290_E	293_D	1.151	1.00
188_L	311_L	1.143	1.00
45_K	77_F	1.142	1.00
129_W	163_Q	1.139	1.00
104_Q	107_R	1.136	1.00
137_E	140_E	1.135	1.00
143_N	146_V	1.112	1.00
38_E	42_P	1.111	1.00
110_D	148_A	1.108	1.00
9_T	153_Y	1.107	1.00
103_A	107_R	1.106	1.00
54_F	209_I	1.105	1.00
186_Y	276_K	1.093	1.00
273_L	282_P	1.092	1.00
146_V	180_V	1.090	1.00
43_I	292_L	1.087	1.00
255_T	265_R	1.083	1.00
54_F	86_A	1.078	1.00
101_S	104_Q	1.076	1.00
142_L	154_I	1.073	1.00
165_A	204_E	1.071	1.00
189_I	251_A	1.069	1.00
185_H	190_Y	1.066	1.00
254_L	265_R	1.060	1.00
126_I	142_L	1.052	1.00
252_E	256_G	1.045	1.00
191_R	315_Y	1.039	1.00
20_C	70_V	1.031	1.00
53_N	84_V	1.031	1.00
45_K	73_A	1.023	1.00
267_Q	297_N	1.022	1.00
256_G	259_E	1.022	1.00
136_E	166_Q	1.014	1.00
166_Q	170_L	1.009	1.00
252_E	255_T	1.000	1.00
42_P	289_E	0.992	1.00
161_A	165_A	0.991	1.00
8_K	180_V	0.991	1.00
145_V	150_K	0.991	1.00
92_R	99_G	0.986	1.00
14_S	53_N	0.978	1.00
156_A	179_F	0.961	1.00
74_L	83_V	0.961	1.00
274_L	298_A	0.958	1.00
292_L	296_L	0.957	1.00
140_E	144_D	0.954	1.00
15_R	274_L	0.953	1.00
188_L	269_A	0.952	1.00
181_S	209_I	0.951	1.00
72_R	76_D	0.950	1.00
199_P	202_Y	0.946	1.00
14_S	52_I	0.937	1.00
102_R	137_E	0.937	1.00
100_L	126_I	0.936	1.00
267_Q	294_E	0.932	1.00
122_D	152_R	0.930	1.00
195_R	199_P	0.928	1.00
9_T	180_V	0.928	1.00
209_I	281_A	0.928	1.00
68_E	114_R	0.914	1.00
145_V	148_A	0.907	1.00
294_E	297_N	0.902	1.00
59_N	104_Q	0.900	1.00
270_L	298_A	0.897	1.00
44_I	55_F	0.895	1.00
106_L	109_I	0.894	1.00
156_A	164_F	0.893	1.00
290_E	294_E	0.889	1.00
107_R	110_D	0.886	1.00
260_E	304_K	0.884	1.00
67_E	115_R	0.883	1.00
141_A	145_V	0.882	1.00
202_Y	279_I	0.874	1.00
15_R	299_V	0.874	1.00
154_I	179_F	0.871	1.00
182_M	201_C	0.871	1.00
42_P	45_K	0.869	1.00
257_V	261_L	0.869	1.00
86_A	209_I	0.865	1.00
309_A	312_E	0.860	1.00
275_S	302_T	0.860	1.00
276_K	308_I	0.859	1.00
224_G	255_T	0.858	1.00
306_E	310_E	0.852	1.00
261_L	304_K	0.845	1.00
158_S	211_W	0.844	1.00
306_E	309_A	0.842	1.00
143_N	154_I	0.842	1.00
140_E	143_N	0.841	1.00
288_R	291_Q	0.834	1.00
166_Q	169_E	0.832	1.00
48_L	79_R	0.826	1.00
86_A	123_I	0.826	1.00
200_L	203_Q	0.825	1.00
99_G	104_Q	0.824	1.00
106_L	145_V	0.824	1.00
9_T	146_V	0.823	1.00
194_E	199_P	0.821	1.00
198_L	208_V	0.820	1.00
164_F	206_V	0.815	1.00
20_C	66_S	0.814	1.00
18_L	47_A	0.803	1.00
37_E	65_S	0.797	1.00
113_L	150_K	0.794	1.00
191_R	312_E	0.784	1.00
213_P	284_I	0.781	1.00
128_R	158_S	0.779	1.00
275_S	305_P	0.769	1.00
161_A	197_M	0.767	1.00
269_A	273_L	0.765	1.00
57_T	70_V	0.760	1.00
17_C	284_I	0.758	1.00
168_L	178_Q	0.756	1.00
46_R	292_L	0.756	1.00
224_G	252_E	0.754	1.00
245_E	249_Q	0.754	1.00
18_L	23_F	0.753	1.00
186_Y	198_L	0.752	1.00
59_N	99_G	0.748	1.00
139_L	167_A	0.744	1.00
113_L	118_M	0.743	1.00
87_T	124_L	0.734	1.00
76_D	79_R	0.732	1.00
50_G	297_N	0.727	1.00
59_N	115_R	0.727	1.00
59_N	111_D	0.716	1.00
210_P	213_P	0.713	1.00
139_L	179_F	0.713	1.00
197_M	201_C	0.708	1.00
303_L	308_I	0.708	1.00
263_A	300_D	0.707	1.00
210_P	282_P	0.707	1.00
272_W	312_E	0.706	1.00
156_A	182_M	0.706	1.00
109_I	150_K	0.704	1.00
40_S	69_I	0.701	1.00
81_E	120_Y	0.700	1.00
207_A	280_A	0.696	1.00
263_A	297_N	0.696	1.00
271_A	298_A	0.695	1.00
52_I	296_L	0.694	1.00
191_R	194_E	0.690	1.00
100_L	138_T	0.689	1.00
139_L	154_I	0.689	1.00
253_R	314_P	0.689	1.00
105_I	145_V	0.687	1.00
11_L	152_R	0.686	1.00
16_L	274_L	0.685	1.00
261_L	268_V	0.685	1.00
287_S	291_Q	0.683	1.00
201_C	206_V	0.682	1.00
249_Q	252_E	0.681	1.00
108_S	111_D	0.680	1.00
43_I	289_E	0.673	1.00
45_K	79_R	0.673	1.00
254_L	311_L	0.671	1.00
48_L	55_F	0.670	1.00
135_I	170_L	0.670	1.00
44_I	48_L	0.669	1.00
156_A	159_M	0.669	1.00
257_V	307_Q	0.667	1.00
266_A	294_E	0.665	1.00
23_F	43_I	0.665	1.00
138_T	141_A	0.662	1.00
38_E	41_R	0.658	1.00
48_L	77_F	0.655	1.00
254_L	269_A	0.654	1.00
53_N	82_D	0.653	1.00
273_L	280_A	0.653	1.00
105_I	138_T	0.652	1.00
291_Q	294_E	0.651	1.00
101_S	138_T	0.650	1.00
198_L	276_K	0.650	1.00
161_A	196_E	0.649	1.00
21_M	212_S	0.645	1.00
186_Y	273_L	0.644	1.00
268_V	303_L	0.644	1.00
268_V	301_I	0.640	1.00
259_E	262_G	0.638	1.00
112_S	124_L	0.637	1.00
146_V	153_Y	0.634	1.00
213_P	273_L	0.634	1.00
39_S	289_E	0.633	1.00
13_V	281_A	0.626	1.00
263_A	271_A	0.625	1.00
60_S	90_F	0.624	1.00
130_D	133_T	0.620	1.00
142_L	146_V	0.616	1.00
73_A	77_F	0.615	1.00
50_G	292_L	0.614	1.00
165_A	168_L	0.612	1.00
257_V	310_E	0.610	1.00
79_R	83_V	0.610	1.00
146_V	151_A	0.609	1.00
186_Y	208_V	0.609	1.00
248_A	252_E	0.607	1.00
105_I	141_A	0.607	1.00
89_V	100_L	0.607	1.00
258_S	265_R	0.602	1.00
125_Q	155_G	0.602	1.00
17_C	281_A	0.600	1.00
303_L	307_Q	0.598	1.00
135_I	138_T	0.596	1.00
109_I	113_L	0.594	1.00
113_L	121_V	0.594	1.00
251_A	255_T	0.592	1.00
43_I	286_T	0.588	1.00
258_S	268_V	0.587	1.00
268_V	307_Q	0.586	1.00
191_R	195_R	0.580	1.00
106_L	150_K	0.575	1.00
22_T	216_R	0.573	1.00
121_V	124_L	0.570	1.00
188_L	272_W	0.569	1.00
13_V	54_F	0.568	1.00
25_E	69_I	0.566	1.00
56_D	183_Q	0.565	1.00
186_Y	191_R	0.563	1.00
8_K	205_G	0.558	1.00
8_K	178_Q	0.557	1.00
113_L	120_Y	0.556	1.00
23_F	40_S	0.556	1.00
124_L	151_A	0.555	1.00
186_Y	280_A	0.555	1.00
17_C	283_I	0.555	1.00
48_L	53_N	0.554	1.00
274_L	282_P	0.553	1.00
48_L	82_D	0.552	1.00
49_E	289_E	0.551	1.00
307_Q	310_E	0.550	1.00
168_L	206_V	0.548	1.00
65_S	69_I	0.547	1.00
163_Q	166_Q	0.545	1.00
257_V	314_P	0.544	1.00
268_V	311_L	0.542	1.00
188_L	315_Y	0.541	1.00
156_A	167_A	0.540	1.00
271_A	302_T	0.538	1.00
44_I	70_V	0.537	1.00
89_V	108_S	0.537	1.00
167_A	179_F	0.536	1.00
258_S	261_L	0.534	1.00
48_L	73_A	0.534	1.00
276_K	280_A	0.532	1.00
289_E	292_L	0.531	1.00
212_S	216_R	0.531	1.00
189_I	218_R	0.531	1.00
261_L	301_I	0.528	1.00
136_E	140_E	0.528	1.00
64_G	115_R	0.527	1.00
67_E	87_T	0.527	1.00
126_I	138_T	0.525	1.00
55_F	74_L	0.524	1.00
249_Q	253_R	0.524	1.00
113_L	119_D	0.524	1.00
7_G	13_V	0.522	1.00
37_E	69_I	0.522	1.00
257_V	260_E	0.521	1.00
210_P	279_I	0.521	1.00
267_Q	301_I	0.521	1.00
135_I	163_Q	0.520	1.00
54_F	84_V	0.520	1.00
59_N	90_F	0.517	1.00
91_H	100_L	0.517	1.00
57_T	66_S	0.516	1.00
18_L	43_I	0.516	1.00
271_A	299_V	0.515	1.00
218_R	247_D	0.514	1.00
254_L	258_S	0.513	1.00
129_W	159_M	0.513	1.00
146_V	178_Q	0.512	1.00
109_I	141_A	0.511	1.00
80_R	122_D	0.510	1.00
154_I	177_A	0.510	1.00
102_R	105_I	0.509	1.00
91_H	128_R	0.506	1.00
218_R	251_A	0.504	1.00
70_V	73_A	0.503	1.00
147_K	177_A	0.501	1.00
7_G	207_A	0.501	1.00
124_L	142_L	0.501	1.00
308_I	312_E	0.500	1.00
135_I	166_Q	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	0.9475	100	0.101	Contact Map
1pz1A	1	0.9691	100	0.102	Contact Map
4xk2A	5	0.9198	100	0.104	Contact Map
3eauA	3	0.966	100	0.105	Contact Map
3lutA	3	0.963	100	0.105	Contact Map
3v0sA	1	0.8272	100	0.107	Contact Map
1lqaA	2	0.9722	100	0.108	Contact Map
3n2tA	1	0.9599	100	0.114	Contact Map
3erpA	6	0.9043	100	0.121	Contact Map
3n6qA	5	0.9105	100	0.126	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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