YDGJ - ECOLI - GREMLIN Contacts

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YDGJ - Uncharacterized oxidoreductase YdgJ

UniProt:	P77376	Sequences: MSDNIRVGLIGYGYASKTFHAPLIAGTPGQELAVISSSDETKVKADWPTVTVVSEPKHLFNDPNIDLIVIPTPNDTHFPLAKAALEAGKHVVVDKPFTVTLSQARELDALAKSLGRVLSVFHNRRWDSDFLTLKGLLAEGVLGEVAYFESHFDRFRPQVRDRWREQGGPGSGIWYDLAPHLLDQAITLFGLPVSMTVDLAQLRPGAQSTDYFHAILSYPQRRVILHGTMLAAAESARYIVHGSRGSYVKYGLDPQEERLKNGERLPQEDWGYDMRDGVLTRVEGEERVEETLLTVPGNYPAYYAAIRDALNGDGENPVPASQAIQVMELIELGIESAKHRATLCLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13931
Length:	346 (312)
Sequences:	25132 (18487)
Seq/√Len:	1046.6

ECOLI - YDGJ YCJS YGJR YHHX YJHC YCEM
BACSU - IOLW YRBE IOLX YFII YULF NTDC IOLG YTET
SULSO - Q97UH0 Q97UJ6 Q97UK0 Q97UK3 Q97UJ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_K	83_A	3.116	1.00
125_R	183_D	2.883	1.00
82_K	110_L	2.821	1.00
78_F	106_E	2.805	1.00
6_R	31_E	2.771	1.00
194_S	217_S	2.758	1.00
132_T	135_G	2.729	1.00
144_E	243_S	2.697	1.00
105_R	324_I	2.687	1.00
40_E	44_K	2.638	1.00
86_E	110_L	2.628	1.00
193_V	219_P	2.455	1.00
72_T	80_L	2.437	1.00
134_K	138_A	2.404	1.00
78_F	103_Q	2.392	1.00
8_G	59_L	2.383	1.00
82_K	86_E	2.368	1.00
82_K	106_E	2.348	1.00
90_H	117_V	2.325	1.00
214_A	333_G	2.285	1.00
85_L	116_R	2.285	1.00
55_E	58_H	2.196	1.00
34_V	53_V	2.140	1.00
76_T	80_L	2.137	1.00
109_A	113_S	2.073	1.00
112_K	321_S	2.048	1.00
135_G	139_E	2.034	1.00
308_D	312_G	2.024	1.00
78_F	82_K	2.003	1.00
51_T	62_D	1.992	1.00
132_T	136_L	1.990	1.00
81_A	93_V	1.976	1.00
85_L	111_A	1.938	1.00
67_L	306_I	1.923	1.00
105_R	109_A	1.898	1.00
105_R	328_E	1.885	1.00
110_L	114_L	1.875	1.00
79_P	83_A	1.853	1.00
39_D	42_K	1.848	1.00
72_T	76_T	1.830	1.00
142_L	242_G	1.780	1.00
86_E	114_L	1.773	1.00
8_G	65_I	1.770	1.00
90_H	116_R	1.760	1.00
24_I	69_V	1.725	1.00
101_L	331_E	1.715	1.00
7_V	67_L	1.715	1.00
68_I	84_A	1.710	1.00
30_Q	307_R	1.667	1.00
81_A	107_L	1.665	1.00
27_T	304_A	1.663	1.00
118_L	320_A	1.652	1.00
65_I	89_K	1.646	1.00
100_T	103_Q	1.642	1.00
54_S	58_H	1.635	1.00
61_N	87_A	1.611	1.00
60_F	84_A	1.596	1.00
199_L	337_A	1.581	1.00
29_G	311_N	1.579	1.00
191_L	325_Q	1.575	1.00
133_L	247_Y	1.573	1.00
134_K	187_T	1.570	1.00
86_E	113_S	1.553	1.00
121_F	302_Y	1.549	1.00
193_V	217_S	1.547	1.00
56_P	83_A	1.521	1.00
108_D	324_I	1.515	1.00
117_V	313_D	1.512	1.00
325_Q	328_E	1.510	1.00
186_I	191_L	1.479	1.00
136_L	141_V	1.477	1.00
99_V	103_Q	1.469	1.00
191_L	219_P	1.455	1.00
108_D	320_A	1.447	1.00
53_V	62_D	1.438	1.00
146_A	243_S	1.433	1.00
78_F	107_L	1.432	1.00
58_H	61_N	1.432	1.00
110_L	113_S	1.431	1.00
57_K	61_N	1.424	1.00
149_E	239_I	1.408	1.00
40_E	54_S	1.399	1.00
98_T	107_L	1.398	1.00
85_L	114_L	1.398	1.00
98_T	104_A	1.380	1.00
43_V	52_V	1.371	1.00
6_R	33_A	1.359	1.00
53_V	59_L	1.357	1.00
83_A	86_E	1.352	1.00
142_L	245_G	1.339	1.00
308_D	314_G	1.333	1.00
6_R	66_D	1.322	1.00
305_A	309_A	1.318	1.00
186_I	325_Q	1.313	1.00
104_A	324_I	1.311	1.00
239_I	248_V	1.308	1.00
83_A	87_A	1.301	1.00
36_S	56_P	1.300	1.00
12_Y	35_I	1.291	1.00
58_H	62_D	1.290	1.00
101_L	105_R	1.281	1.00
101_L	328_E	1.281	1.00
145_V	240_V	1.280	1.00
198_D	217_S	1.277	1.00
192_P	218_Y	1.266	1.00
182_L	329_L	1.265	1.00
70_I	80_L	1.255	1.00
84_A	91_V	1.242	1.00
63_P	89_K	1.220	1.00
56_P	80_L	1.208	1.00
36_S	59_L	1.205	1.00
305_A	317_P	1.205	1.00
88_G	114_L	1.202	1.00
70_I	81_A	1.196	1.00
106_E	109_A	1.196	1.00
59_L	65_I	1.194	1.00
34_V	59_L	1.186	1.00
85_L	110_L	1.181	1.00
186_I	218_Y	1.178	1.00
166_Q	169_P	1.164	1.00
75_D	169_P	1.163	1.00
73_P	76_T	1.160	1.00
41_T	44_K	1.158	1.00
237_R	248_V	1.158	1.00
189_F	222_R	1.157	1.00
108_D	321_S	1.151	1.00
64_N	89_K	1.145	1.00
148_F	189_F	1.142	1.00
319_P	322_Q	1.141	1.00
136_L	139_E	1.136	1.00
26_G	300_P	1.134	1.00
196_T	215_I	1.134	1.00
7_V	30_Q	1.134	1.00
149_E	226_H	1.128	1.00
97_F	104_A	1.127	1.00
109_A	112_K	1.127	1.00
5_I	311_N	1.117	1.00
106_E	110_L	1.114	1.00
304_A	308_D	1.108	1.00
331_E	335_E	1.107	1.00
5_I	67_L	1.106	1.00
186_I	322_Q	1.105	1.00
90_H	313_D	1.105	1.00
47_W	50_V	1.096	1.00
60_F	83_A	1.090	1.00
92_V	121_F	1.090	1.00
130_F	187_T	1.088	1.00
82_K	107_L	1.085	1.00
104_A	327_M	1.077	1.00
142_L	247_Y	1.072	1.00
103_Q	106_E	1.068	1.00
332_L	335_E	1.067	1.00
56_P	60_F	1.066	1.00
307_R	311_N	1.065	1.00
60_F	87_A	1.061	1.00
142_L	145_V	1.053	1.00
92_V	302_Y	1.052	1.00
90_H	310_L	1.044	1.00
20_H	69_V	1.037	1.00
5_I	310_L	1.035	1.00
108_D	112_K	1.034	1.00
34_V	65_I	1.030	1.00
93_V	118_L	1.020	1.00
10_I	80_L	1.020	1.00
335_E	338_K	1.014	1.00
98_T	103_Q	1.012	1.00
62_D	65_I	1.011	1.00
42_K	45_A	1.009	1.00
126_W	305_A	1.009	1.00
305_A	314_G	1.006	1.00
135_G	138_A	1.001	1.00
107_L	118_L	0.982	1.00
43_V	54_S	0.982	1.00
125_R	322_Q	0.980	1.00
102_S	105_R	0.977	1.00
305_A	308_D	0.975	1.00
332_L	336_S	0.973	1.00
131_L	317_P	0.968	1.00
133_L	249_K	0.953	1.00
111_A	114_L	0.953	1.00
81_A	91_V	0.949	1.00
97_F	320_A	0.948	1.00
22_P	26_G	0.946	1.00
192_P	216_L	0.945	1.00
80_L	83_A	0.943	1.00
101_L	324_I	0.938	1.00
145_V	189_F	0.937	1.00
53_V	58_H	0.933	1.00
41_T	45_A	0.931	1.00
17_K	46_D	0.928	1.00
78_F	98_T	0.916	1.00
145_V	242_G	0.914	1.00
123_N	298_N	0.913	1.00
321_S	325_Q	0.913	1.00
300_P	304_A	0.913	1.00
102_S	106_E	0.913	1.00
301_A	304_A	0.910	1.00
119_S	306_I	0.910	1.00
51_T	64_N	0.906	1.00
40_E	43_V	0.903	1.00
97_F	118_L	0.903	1.00
85_L	91_V	0.901	1.00
12_Y	37_S	0.900	1.00
70_I	84_A	0.896	1.00
308_D	313_D	0.895	1.00
148_F	240_V	0.884	1.00
196_T	336_S	0.883	1.00
46_D	49_T	0.881	1.00
309_A	312_G	0.879	1.00
150_S	238_Y	0.878	1.00
197_V	333_G	0.878	1.00
182_L	330_I	0.874	1.00
81_A	85_L	0.873	1.00
93_V	97_F	0.866	1.00
8_G	34_V	0.864	1.00
20_H	303_Y	0.862	1.00
213_H	224_I	0.861	1.00
69_V	303_Y	0.859	1.00
76_T	79_P	0.857	1.00
44_K	52_V	0.850	1.00
62_D	89_K	0.849	1.00
143_G	242_G	0.847	1.00
37_S	42_K	0.846	1.00
111_A	118_L	0.845	1.00
328_E	332_L	0.843	1.00
117_V	310_L	0.843	1.00
334_I	338_K	0.842	1.00
166_Q	207_Q	0.842	1.00
143_G	245_G	0.841	1.00
8_G	36_S	0.838	1.00
167_G	338_K	0.837	1.00
309_A	316_N	0.836	1.00
167_G	207_Q	0.836	1.00
33_A	51_T	0.835	1.00
6_R	65_I	0.833	1.00
192_P	219_P	0.832	1.00
40_E	52_V	0.831	1.00
105_R	108_D	0.829	1.00
192_P	329_L	0.827	1.00
7_V	24_I	0.821	1.00
33_A	64_N	0.820	1.00
239_I	246_S	0.818	1.00
117_V	309_A	0.816	1.00
185_A	218_Y	0.814	1.00
93_V	107_L	0.814	1.00
171_S	175_Y	0.812	1.00
74_N	176_D	0.809	1.00
24_I	30_Q	0.809	1.00
131_L	135_G	0.807	1.00
37_S	43_V	0.805	1.00
111_A	116_R	0.805	1.00
15_A	20_H	0.801	1.00
111_A	320_A	0.799	1.00
16_S	22_P	0.799	1.00
24_I	303_Y	0.799	1.00
149_E	224_I	0.791	1.00
29_G	304_A	0.790	1.00
119_S	309_A	0.784	1.00
99_V	170_G	0.783	1.00
85_L	118_L	0.782	1.00
237_R	250_Y	0.781	1.00
9_L	21_A	0.781	1.00
186_I	326_V	0.780	1.00
16_S	71_P	0.779	1.00
148_F	185_A	0.772	1.00
138_A	190_G	0.771	1.00
67_L	90_H	0.770	1.00
137_L	242_G	0.768	1.00
27_T	30_Q	0.766	1.00
15_A	71_P	0.761	1.00
315_E	319_P	0.760	1.00
33_A	65_I	0.757	1.00
198_D	215_I	0.756	1.00
15_A	299_Y	0.756	1.00
97_F	120_V	0.755	1.00
122_H	179_P	0.754	1.00
10_I	56_P	0.752	1.00
21_A	32_L	0.748	1.00
33_A	62_D	0.747	1.00
104_A	108_D	0.746	1.00
150_S	181_L	0.741	1.00
78_F	110_L	0.740	1.00
306_I	310_L	0.740	1.00
309_A	314_G	0.740	1.00
120_V	323_A	0.736	1.00
8_G	68_I	0.735	1.00
179_P	326_V	0.728	1.00
48_P	51_T	0.726	1.00
173_I	227_G	0.726	1.00
10_I	36_S	0.726	1.00
172_G	209_T	0.723	1.00
59_L	62_D	0.722	1.00
324_I	328_E	0.721	1.00
189_F	218_Y	0.718	1.00
174_W	330_I	0.717	1.00
144_E	244_R	0.712	1.00
12_Y	43_V	0.705	1.00
320_A	323_A	0.704	1.00
327_M	331_E	0.703	1.00
27_T	307_R	0.701	1.00
88_G	116_R	0.700	1.00
82_K	85_L	0.699	1.00
93_V	120_V	0.699	1.00
77_H	93_V	0.698	1.00
10_I	72_T	0.698	1.00
131_L	301_A	0.698	1.00
188_L	240_V	0.695	1.00
200_A	217_S	0.694	1.00
125_R	187_T	0.694	1.00
85_L	107_L	0.692	1.00
137_L	240_V	0.691	1.00
29_G	308_D	0.688	1.00
144_E	220_Q	0.684	1.00
6_R	64_N	0.680	1.00
130_F	184_Q	0.680	1.00
194_S	198_D	0.678	1.00
299_Y	302_Y	0.675	1.00
197_V	214_A	0.674	1.00
191_L	328_E	0.673	1.00
124_R	127_D	0.672	1.00
198_D	223_V	0.671	1.00
7_V	307_R	0.670	1.00
183_D	326_V	0.668	1.00
241_H	246_S	0.667	1.00
122_H	183_D	0.667	1.00
92_V	119_S	0.665	1.00
117_V	315_E	0.664	1.00
209_T	334_I	0.663	1.00
174_W	212_F	0.662	1.00
134_K	188_L	0.658	1.00
17_K	45_A	0.658	1.00
322_Q	325_Q	0.657	1.00
178_A	181_L	0.656	1.00
150_S	185_A	0.656	1.00
29_G	307_R	0.655	1.00
202_L	210_D	0.654	1.00
197_V	212_F	0.654	1.00
79_P	106_E	0.653	1.00
178_A	227_G	0.652	1.00
17_K	42_K	0.648	1.00
81_A	118_L	0.645	1.00
7_V	69_V	0.644	1.00
67_L	310_L	0.641	1.00
176_D	229_M	0.640	1.00
305_A	316_N	0.639	1.00
228_T	231_A	0.638	1.00
123_N	299_Y	0.634	1.00
186_I	329_L	0.634	1.00
53_V	63_P	0.629	1.00
261_N	264_R	0.628	1.00
31_E	50_V	0.627	1.00
89_K	116_R	0.625	1.00
210_D	230_L	0.624	1.00
35_I	43_V	0.622	1.00
183_D	187_T	0.619	1.00
117_V	316_N	0.619	1.00
56_P	84_A	0.618	1.00
182_L	333_G	0.614	1.00
137_L	188_L	0.612	1.00
35_I	52_V	0.612	1.00
119_S	305_A	0.611	1.00
15_A	94_D	0.610	1.00
68_I	89_K	0.608	1.00
214_A	225_L	0.608	1.00
122_H	326_V	0.604	1.00
124_R	183_D	0.604	1.00
258_R	261_N	0.601	1.00
151_H	226_H	0.599	1.00
17_K	47_W	0.599	1.00
86_E	106_E	0.598	1.00
57_K	79_P	0.596	1.00
211_Y	228_T	0.595	1.00
32_L	49_T	0.594	1.00
39_D	44_K	0.593	1.00
147_Y	241_H	0.592	1.00
69_V	92_V	0.592	1.00
326_V	330_I	0.590	1.00
180_H	183_D	0.589	1.00
81_A	111_A	0.587	1.00
95_K	176_D	0.584	1.00
133_L	188_L	0.581	1.00
216_L	225_L	0.580	1.00
196_T	217_S	0.579	1.00
131_L	187_T	0.578	1.00
38_S	72_T	0.578	1.00
203_R	210_D	0.577	1.00
100_T	331_E	0.577	1.00
199_L	212_F	0.575	1.00
147_Y	223_V	0.574	1.00
174_W	214_A	0.573	1.00
79_P	82_K	0.572	1.00
108_D	111_A	0.571	1.00
34_V	51_T	0.568	1.00
308_D	311_N	0.568	1.00
175_Y	331_E	0.568	1.00
48_P	52_V	0.567	1.00
141_V	144_E	0.567	1.00
70_I	77_H	0.565	1.00
330_I	334_I	0.565	1.00
66_D	311_N	0.563	1.00
17_K	22_P	0.559	1.00
30_Q	67_L	0.558	1.00
119_S	302_Y	0.557	1.00
168_G	207_Q	0.556	1.00
14_Y	19_F	0.556	1.00
13_G	71_P	0.554	1.00
151_H	237_R	0.554	1.00
195_M	329_L	0.552	1.00
140_G	242_G	0.552	1.00
94_D	121_F	0.549	1.00
140_G	144_E	0.548	1.00
20_H	24_I	0.546	1.00
36_S	53_V	0.545	1.00
215_I	224_I	0.544	1.00
164_R	176_D	0.544	1.00
258_R	262_G	0.543	1.00
71_P	94_D	0.543	1.00
257_E	260_K	0.542	1.00
13_G	16_S	0.541	1.00
5_I	30_Q	0.540	1.00
215_I	223_V	0.540	1.00
22_P	25_A	0.539	1.00
218_Y	222_R	0.538	1.00
120_V	180_H	0.538	1.00
147_Y	211_Y	0.535	1.00
131_L	134_K	0.535	1.00
170_G	208_S	0.533	1.00
102_S	331_E	0.530	1.00
97_F	107_L	0.530	1.00
5_I	307_R	0.530	1.00
257_E	261_N	0.529	1.00
297_G	300_P	0.528	1.00
117_V	306_I	0.527	1.00
20_H	71_P	0.526	1.00
75_D	99_V	0.526	1.00
128_S	301_A	0.526	1.00
10_I	68_I	0.526	1.00
185_A	225_L	0.525	1.00
10_I	70_I	0.525	1.00
82_K	114_L	0.522	1.00
189_F	220_Q	0.521	1.00
9_L	69_V	0.521	1.00
126_W	318_V	0.519	1.00
290_E	293_L	0.518	1.00
173_I	177_L	0.518	1.00
122_H	180_H	0.517	1.00
95_K	180_H	0.517	1.00
148_F	238_Y	0.517	1.00
9_L	32_L	0.515	1.00
256_E	259_L	0.515	1.00
72_T	77_H	0.515	1.00
21_A	25_A	0.514	1.00
147_Y	226_H	0.513	1.00
163_W	166_Q	0.513	1.00
27_T	300_P	0.513	1.00
216_L	329_L	0.512	1.00
123_N	180_H	0.512	1.00
329_L	332_L	0.511	1.00
134_K	190_G	0.510	1.00
57_K	87_A	0.510	1.00
259_L	263_E	0.509	1.00
251_G	254_P	0.509	1.00
36_S	54_S	0.508	1.00
51_T	63_P	0.507	1.00
104_A	323_A	0.507	1.00
186_I	192_P	0.503	1.00
111_A	115_G	0.501	1.00
147_Y	224_I	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
3kuxA	2	0.9913	100	0.195	Contact Map
3gdoA	2	0.974	100	0.195	Contact Map
3e82A	2	0.9798	100	0.196	Contact Map
3fhlA	2	0.9624	100	0.204	Contact Map
3dtyA	4	0.9509	100	0.215	Contact Map
1h6dA	8	0.9538	100	0.218	Contact Map
1zh8A	2	0.9017	100	0.219	Contact Map
3v5nA	4	0.9306	100	0.222	Contact Map
3db2A	2	0.9682	100	0.229	Contact Map
2nvwA	3	0.9249	100	0.23	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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