YDBM - BACSU - GREMLIN Contacts

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YDBM - Putative acyl-CoA dehydrogenase YdbM

UniProt:	P96608	Sequences: MSLFIQNDQQRQWMEKIGRIADEFQQTAAEDDEQGRFPAEKIQKLRDAGYTALTLPASHGGGGISVYDMLLFQERLARGDAPTALSIGWHLSVIGELGEGNSWDEDVFAFVAKEVQNGAVINRAATEAKTGSPTRGGRPGTHAVKKDGKWAVNGRKTFTTMSQALDYFLVTAWIEDKQTTGVFLIHKDDPGLSIEETWDMMAMRATGSHDLVLNEVMLDENKLVELLQGPRGAKPNGWLLHIPAIYLGVAQAARDYAVQFASEYSPNSLNGPIKNVPAVQQRTGEMELELLNARHFLFHIAQLYDDPVRRPHLTSELGAAKHIVTNAALSVVDKAMRIVGAKSLERTNPLQRYYRDVRAGLHNPPMDDAVIHKLAAEAFES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	381 (360)
Sequences:	33714 (19303)
Seq/√Len:	1017.4

ECOLI - CAIA YDIO AIDB FADE
BACSU - YDBM ACDC ACDA FADE ACDB
HALSA - Q9HS75 Q9HRI6 Q9HPT2 Q9HRB3 Q9HQF0 Q9HMK7
SULSO - Q97UW6 Q97V73 Q97U78 Q97WQ8 Q97VU6 Q97XW3 Q97YZ6 Q97VV8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
149_K	217_M	4.133	1.00
153_N	215_E	3.842	1.00
289_E	330_S	3.435	1.00
23_E	44_K	3.218	1.00
145_K	220_E	2.931	1.00
193_S	214_N	2.880	1.00
113_K	118_G	2.874	1.00
30_E	34_Q	2.847	1.00
104_D	108_F	2.798	1.00
181_G	223_L	2.772	1.00
18_G	75_R	2.766	1.00
65_S	68_D	2.702	1.00
146_K	217_M	2.550	1.00
282_R	334_K	2.431	1.00
259_Q	263_E	2.365	1.00
113_K	119_A	2.284	1.00
251_Q	294_R	2.263	1.00
155_R	212_V	2.263	1.00
146_K	149_K	2.156	1.00
302_Q	306_D	2.107	1.00
172_A	183_F	2.094	1.00
272_P	275_N	2.045	1.00
104_D	107_V	2.042	1.00
346_R	351_Q	1.977	1.00
261_A	338_I	1.937	1.00
103_W	106_D	1.928	1.00
351_Q	355_R	1.922	1.00
74_E	294_R	1.914	1.00
19_R	22_D	1.901	1.00
168_F	187_K	1.867	1.00
56_P	99_E	1.852	1.00
228_Q	231_R	1.844	1.00
150_W	183_F	1.801	1.00
254_R	290_L	1.796	1.00
155_R	210_D	1.790	1.00
10_Q	68_D	1.788	1.00
326_N	367_D	1.777	1.00
44_K	47_D	1.772	1.00
43_Q	47_D	1.749	1.00
78_R	255_D	1.733	1.00
122_N	168_F	1.713	1.00
251_Q	255_D	1.708	1.00
150_W	220_E	1.704	1.00
75_R	78_R	1.677	1.00
162_S	209_H	1.672	1.00
265_S	272_P	1.665	1.00
151_A	217_M	1.663	1.00
278_A	281_Q	1.650	1.00
219_D	222_K	1.619	1.00
303_L	316_E	1.598	1.00
261_A	279_V	1.597	1.00
144_V	153_N	1.593	1.00
256_Y	349_P	1.589	1.00
127_E	156_K	1.585	1.00
151_A	215_E	1.570	1.00
286_M	331_V	1.570	1.00
109_A	221_N	1.556	1.00
109_A	113_K	1.554	1.00
186_H	222_K	1.547	1.00
189_D	216_V	1.543	1.00
148_G	220_E	1.537	1.00
193_S	212_V	1.534	1.00
57_A	63_G	1.526	1.00
271_G	275_N	1.517	1.00
299_H	303_L	1.515	1.00
292_N	323_I	1.514	1.00
12_Q	15_E	1.504	1.00
153_N	214_N	1.504	1.00
253_A	332_V	1.500	1.00
126_T	158_F	1.494	1.00
10_Q	65_S	1.491	1.00
11_R	14_M	1.488	1.00
113_K	116_Q	1.482	1.00
15_E	19_R	1.472	1.00
220_E	223_L	1.467	1.00
195_E	210_D	1.463	1.00
108_F	112_A	1.459	1.00
268_S	276_V	1.458	1.00
59_H	107_V	1.453	1.00
163_Q	209_H	1.449	1.00
342_K	348_N	1.445	1.00
293_A	324_V	1.441	1.00
80_D	83_T	1.431	1.00
21_A	79_G	1.429	1.00
195_E	212_V	1.429	1.00
279_V	338_I	1.424	1.00
145_K	149_K	1.420	1.00
256_Y	259_Q	1.418	1.00
258_V	262_S	1.408	1.00
12_Q	16_K	1.396	1.00
252_A	256_Y	1.391	1.00
152_V	183_F	1.379	1.00
78_R	251_Q	1.377	1.00
330_S	334_K	1.376	1.00
291_L	299_H	1.375	1.00
10_Q	71_L	1.375	1.00
186_H	189_D	1.367	1.00
329_L	361_L	1.366	1.00
105_E	109_A	1.361	1.00
286_M	334_K	1.354	1.00
322_H	367_D	1.352	1.00
74_E	298_F	1.343	1.00
333_D	358_R	1.341	1.00
143_A	183_F	1.340	1.00
67_Y	302_Q	1.339	1.00
199_D	346_R	1.334	1.00
14_M	75_R	1.326	1.00
218_L	222_K	1.318	1.00
74_E	251_Q	1.307	1.00
17_I	50_Y	1.303	1.00
39_A	43_Q	1.303	1.00
145_K	150_W	1.299	1.00
53_L	72_F	1.298	1.00
148_G	217_M	1.287	1.00
66_V	305_D	1.283	1.00
33_E	199_D	1.278	1.00
105_E	221_N	1.269	1.00
106_D	110_F	1.259	1.00
149_K	220_E	1.258	1.00
250_A	290_L	1.258	1.00
189_D	222_K	1.255	1.00
257_A	335_A	1.252	1.00
174_I	181_G	1.251	1.00
285_E	371_I	1.243	1.00
101_N	235_P	1.233	1.00
187_K	192_L	1.232	1.00
124_A	159_T	1.229	1.00
112_A	116_Q	1.226	1.00
31_D	205_A	1.222	1.00
192_L	216_V	1.214	1.00
107_V	111_V	1.211	1.00
43_Q	46_R	1.209	1.00
250_A	331_V	1.209	1.00
11_R	15_E	1.205	1.00
146_K	151_A	1.205	1.00
238_W	364_P	1.199	1.00
333_D	361_L	1.196	1.00
230_P	234_K	1.192	1.00
254_R	258_V	1.191	1.00
191_G	216_V	1.188	1.00
70_L	301_A	1.185	1.00
129_K	140_G	1.185	1.00
290_L	331_V	1.184	1.00
299_H	302_Q	1.183	1.00
77_A	84_A	1.178	1.00
14_M	71_L	1.173	1.00
114_E	121_I	1.170	1.00
328_A	357_V	1.170	1.00
252_A	353_Y	1.165	1.00
64_I	68_D	1.164	1.00
65_S	305_D	1.164	1.00
244_A	297_L	1.164	1.00
287_E	291_L	1.162	1.00
282_R	368_D	1.161	1.00
144_V	151_A	1.155	1.00
271_G	276_V	1.153	1.00
171_T	182_V	1.147	1.00
236_N	314_T	1.146	1.00
55_L	115_V	1.145	1.00
44_K	48_A	1.144	1.00
256_Y	339_V	1.134	1.00
109_A	222_K	1.134	1.00
119_A	166_D	1.134	1.00
335_A	350_L	1.132	1.00
16_K	48_A	1.131	1.00
303_L	308_V	1.131	1.00
358_R	361_L	1.121	1.00
70_L	244_A	1.117	1.00
110_F	167_Y	1.116	1.00
329_L	333_D	1.115	1.00
29_A	33_E	1.113	1.00
102_S	106_D	1.108	1.00
187_K	194_I	1.105	1.00
27_T	31_D	1.095	1.00
293_A	327_A	1.095	1.00
43_Q	118_G	1.091	1.00
289_E	334_K	1.090	1.00
17_I	21_A	1.079	1.00
318_G	370_V	1.079	1.00
124_A	168_F	1.078	1.00
150_W	174_I	1.075	1.00
170_V	185_I	1.071	1.00
152_V	170_V	1.070	1.00
142_H	153_N	1.067	1.00
288_L	319_A	1.065	1.00
141_T	152_V	1.065	1.00
247_L	290_L	1.061	1.00
217_M	220_E	1.053	1.00
46_R	51_T	1.049	1.00
171_T	180_T	1.046	1.00
361_L	367_D	1.043	1.00
58_S	108_F	1.039	1.00
94_I	121_I	1.036	1.00
105_E	108_F	1.035	1.00
192_L	211_L	1.029	1.00
16_K	50_Y	1.024	1.00
27_T	30_E	1.023	1.00
289_E	327_A	1.022	1.00
121_I	167_Y	1.013	1.00
170_V	213_L	1.013	1.00
144_V	215_E	1.009	1.00
106_D	184_L	1.007	1.00
329_L	354_Y	0.990	1.00
175_E	179_T	0.985	1.00
40_E	43_Q	0.976	1.00
168_F	192_L	0.976	1.00
322_H	371_I	0.975	1.00
295_H	299_H	0.975	1.00
20_I	44_K	0.975	1.00
253_A	353_Y	0.974	1.00
261_A	273_I	0.970	1.00
262_S	274_K	0.967	1.00
326_N	330_S	0.965	1.00
332_V	357_V	0.963	1.00
150_W	223_L	0.963	1.00
94_I	169_L	0.961	1.00
247_L	297_L	0.956	1.00
258_V	283_T	0.954	1.00
326_N	361_L	0.953	1.00
124_A	213_L	0.948	1.00
109_A	186_H	0.947	1.00
327_A	330_S	0.944	1.00
246_Y	360_G	0.944	1.00
147_D	217_M	0.941	1.00
82_P	205_A	0.938	1.00
106_D	222_K	0.938	1.00
152_V	172_A	0.938	1.00
183_F	223_L	0.936	1.00
143_A	172_A	0.936	1.00
367_D	371_I	0.929	1.00
17_I	72_F	0.928	1.00
203_M	359_A	0.923	1.00
285_E	289_E	0.923	1.00
158_F	342_K	0.921	1.00
325_T	367_D	0.921	1.00
32_D	355_R	0.920	1.00
168_F	211_L	0.913	1.00
39_A	166_D	0.905	1.00
55_L	95_G	0.904	1.00
201_M	354_Y	0.901	1.00
300_I	320_A	0.899	1.00
144_V	175_E	0.899	1.00
167_Y	186_H	0.893	1.00
20_I	48_A	0.890	1.00
56_P	59_H	0.889	1.00
157_T	210_D	0.888	1.00
58_S	104_D	0.887	1.00
152_V	218_L	0.886	1.00
359_A	363_N	0.885	1.00
162_S	194_I	0.885	1.00
287_E	319_A	0.883	1.00
67_Y	305_D	0.882	1.00
261_A	274_K	0.880	1.00
103_W	107_V	0.877	1.00
326_N	371_I	0.874	1.00
132_S	369_A	0.871	1.00
33_E	346_R	0.871	1.00
255_D	259_Q	0.869	1.00
336_M	354_Y	0.857	1.00
202_A	356_D	0.857	1.00
181_G	227_L	0.852	1.00
158_F	345_E	0.851	1.00
259_Q	262_S	0.848	1.00
122_N	165_L	0.847	1.00
360_G	363_N	0.845	1.00
122_N	187_K	0.844	1.00
329_L	358_R	0.843	1.00
27_T	40_E	0.841	1.00
201_M	351_Q	0.841	1.00
190_P	217_M	0.840	1.00
289_E	323_I	0.840	1.00
21_A	76_L	0.839	1.00
166_D	188_D	0.835	1.00
249_V	328_A	0.835	1.00
173_W	180_T	0.833	1.00
257_A	338_I	0.829	1.00
101_N	232_G	0.825	1.00
167_Y	184_L	0.824	1.00
281_Q	372_H	0.823	1.00
280_Q	372_H	0.819	1.00
16_K	19_R	0.818	1.00
119_A	167_Y	0.817	1.00
183_F	218_L	0.816	1.00
327_A	331_V	0.814	1.00
30_E	33_E	0.814	1.00
281_Q	285_E	0.814	1.00
336_M	350_L	0.813	1.00
20_I	45_L	0.813	1.00
173_W	176_D	0.812	1.00
257_A	339_V	0.810	1.00
282_R	338_I	0.808	1.00
332_V	353_Y	0.807	1.00
100_G	235_P	0.807	1.00
261_A	283_T	0.806	1.00
194_I	211_L	0.801	1.00
67_Y	298_F	0.800	1.00
249_V	357_V	0.799	1.00
291_L	294_R	0.797	1.00
45_L	50_Y	0.797	1.00
249_V	353_Y	0.796	1.00
67_Y	71_L	0.793	1.00
213_L	216_V	0.793	1.00
54_T	69_M	0.793	1.00
250_A	327_A	0.791	1.00
333_D	354_Y	0.790	1.00
124_A	170_V	0.789	1.00
59_H	104_D	0.786	1.00
14_M	18_G	0.780	1.00
291_L	295_H	0.780	1.00
10_Q	67_Y	0.779	1.00
332_V	354_Y	0.776	1.00
242_I	364_P	0.776	1.00
40_E	44_K	0.772	1.00
149_K	219_D	0.772	1.00
247_L	293_A	0.772	1.00
143_A	150_W	0.771	1.00
243_P	320_A	0.767	1.00
41_K	83_T	0.766	1.00
285_E	334_K	0.766	1.00
257_A	261_A	0.766	1.00
143_A	174_I	0.765	1.00
169_L	182_V	0.763	1.00
141_T	144_V	0.762	1.00
71_L	75_R	0.762	1.00
256_Y	353_Y	0.760	1.00
139_P	171_T	0.757	1.00
254_R	287_E	0.755	1.00
288_L	323_I	0.755	1.00
354_Y	358_R	0.755	1.00
286_M	335_A	0.753	1.00
149_K	221_N	0.752	1.00
323_I	327_A	0.750	1.00
141_T	156_K	0.748	1.00
203_M	363_N	0.745	1.00
58_S	107_V	0.741	1.00
273_I	276_V	0.739	1.00
166_D	187_K	0.736	1.00
296_F	320_A	0.735	1.00
110_F	184_L	0.734	1.00
124_A	211_L	0.731	1.00
253_A	335_A	0.727	1.00
25_Q	28_A	0.727	1.00
174_I	179_T	0.727	1.00
223_L	226_L	0.726	1.00
251_Q	287_E	0.725	1.00
372_H	376_A	0.724	1.00
181_G	225_E	0.724	1.00
260_F	342_K	0.724	1.00
330_S	333_D	0.722	1.00
285_E	330_S	0.721	1.00
296_F	319_A	0.721	1.00
337_R	358_R	0.721	1.00
277_P	281_Q	0.719	1.00
78_R	252_A	0.719	1.00
20_I	23_E	0.718	1.00
29_A	352_R	0.717	1.00
352_R	356_D	0.715	1.00
71_L	298_F	0.715	1.00
175_E	227_L	0.715	1.00
152_V	185_I	0.714	1.00
189_D	192_L	0.714	1.00
110_F	222_K	0.714	1.00
276_V	280_Q	0.711	1.00
53_L	64_I	0.711	1.00
163_Q	207_G	0.708	1.00
127_E	141_T	0.703	1.00
332_V	350_L	0.703	1.00
292_N	296_F	0.700	1.00
21_A	24_F	0.700	1.00
204_R	346_R	0.698	1.00
288_L	322_H	0.697	1.00
139_P	180_T	0.696	1.00
95_G	114_E	0.695	1.00
188_D	192_L	0.693	1.00
370_V	373_K	0.691	1.00
58_S	61_G	0.691	1.00
148_G	221_N	0.688	1.00
58_S	63_G	0.685	1.00
301_A	305_D	0.682	1.00
243_P	297_L	0.679	1.00
336_M	343_S	0.678	1.00
14_M	74_E	0.675	1.00
169_L	224_V	0.674	1.00
56_P	61_G	0.674	1.00
41_K	44_K	0.673	1.00
123_R	233_A	0.669	1.00
24_F	41_K	0.668	1.00
228_Q	232_G	0.668	1.00
125_A	134_T	0.667	1.00
102_S	107_V	0.666	1.00
173_W	179_T	0.665	1.00
39_A	120_V	0.664	1.00
297_L	324_V	0.664	1.00
55_L	59_H	0.663	1.00
114_E	167_Y	0.663	1.00
328_A	332_V	0.659	1.00
339_V	350_L	0.657	1.00
139_P	173_W	0.656	1.00
236_N	317_L	0.656	1.00
246_Y	325_T	0.654	1.00
294_R	298_F	0.653	1.00
313_L	316_E	0.653	1.00
243_P	324_V	0.652	1.00
366_M	369_A	0.652	1.00
159_T	211_L	0.644	1.00
280_Q	375_A	0.642	1.00
145_K	151_A	0.640	1.00
155_R	195_E	0.637	1.00
289_E	292_N	0.636	1.00
85_L	203_M	0.634	1.00
240_L	301_A	0.631	1.00
269_L	276_V	0.625	1.00
22_D	26_Q	0.622	1.00
13_W	72_F	0.621	1.00
139_P	143_A	0.619	1.00
110_F	119_A	0.619	1.00
244_A	248_G	0.617	1.00
146_K	220_E	0.616	1.00
252_A	349_P	0.616	1.00
202_A	344_L	0.615	1.00
282_R	285_E	0.613	1.00
141_T	213_L	0.613	1.00
9_Q	12_Q	0.612	1.00
312_H	316_E	0.612	1.00
279_V	283_T	0.610	1.00
257_A	286_M	0.606	1.00
29_A	349_P	0.605	1.00
18_G	78_R	0.605	1.00
250_A	293_A	0.604	1.00
296_F	323_I	0.603	1.00
162_S	211_L	0.601	1.00
13_W	68_D	0.598	1.00
319_A	374_L	0.597	1.00
183_F	220_E	0.596	1.00
95_G	111_V	0.596	1.00
106_D	109_A	0.594	1.00
250_A	253_A	0.594	1.00
39_A	164_A	0.592	1.00
299_H	316_E	0.591	1.00
322_H	374_L	0.591	1.00
199_D	204_R	0.590	1.00
69_M	241_H	0.590	1.00
282_R	337_R	0.588	1.00
341_A	344_L	0.587	1.00
28_A	352_R	0.586	1.00
200_M	208_S	0.586	1.00
192_L	213_L	0.584	1.00
164_A	207_G	0.582	1.00
252_A	255_D	0.581	1.00
329_L	357_V	0.580	1.00
170_V	216_V	0.579	1.00
147_D	151_A	0.578	1.00
293_A	323_I	0.578	1.00
173_W	177_K	0.576	1.00
296_F	300_I	0.574	1.00
9_Q	68_D	0.574	1.00
94_I	97_L	0.572	1.00
185_I	213_L	0.572	1.00
174_I	183_F	0.572	1.00
24_F	27_T	0.572	1.00
289_E	326_N	0.570	1.00
23_E	27_T	0.568	1.00
94_I	114_E	0.568	1.00
304_Y	313_L	0.566	1.00
36_R	39_A	0.562	1.00
325_T	360_G	0.561	1.00
293_A	320_A	0.561	1.00
349_P	352_R	0.559	1.00
268_S	273_I	0.558	1.00
13_W	17_I	0.557	1.00
160_T	208_S	0.556	1.00
358_R	362_H	0.555	1.00
99_E	107_V	0.555	1.00
81_A	249_V	0.555	1.00
45_L	83_T	0.554	1.00
142_H	176_D	0.554	1.00
59_H	112_A	0.552	1.00
349_P	353_Y	0.552	1.00
260_F	348_N	0.551	1.00
226_L	232_G	0.551	1.00
183_F	222_K	0.551	1.00
264_Y	341_A	0.551	1.00
35_G	204_R	0.551	1.00
66_V	304_Y	0.550	1.00
229_G	232_G	0.550	1.00
264_Y	269_L	0.549	1.00
98_G	102_S	0.548	1.00
201_M	355_R	0.547	1.00
291_L	296_F	0.545	1.00
185_I	216_V	0.545	1.00
251_Q	290_L	0.544	1.00
125_A	171_T	0.544	1.00
23_E	26_Q	0.542	1.00
141_T	145_K	0.541	1.00
285_E	288_L	0.541	1.00
128_A	155_R	0.540	1.00
35_G	199_D	0.538	1.00
288_L	292_N	0.536	1.00
18_G	79_G	0.536	1.00
130_T	140_G	0.535	1.00
279_V	282_R	0.534	1.00
16_K	62_G	0.533	1.00
32_D	204_R	0.533	1.00
96_E	100_G	0.533	1.00
97_L	101_N	0.532	1.00
286_M	338_I	0.532	1.00
369_A	372_H	0.531	1.00
35_G	346_R	0.529	1.00
71_L	74_E	0.528	1.00
109_A	112_A	0.527	1.00
227_L	231_R	0.526	1.00
145_K	183_F	0.526	1.00
141_T	154_G	0.526	1.00
142_H	175_E	0.526	1.00
145_K	148_G	0.524	1.00
52_A	115_V	0.524	1.00
322_H	326_N	0.523	1.00
52_A	62_G	0.522	1.00
293_A	331_V	0.522	1.00
80_D	205_A	0.519	1.00
285_E	326_N	0.517	1.00
247_L	251_Q	0.516	1.00
86_S	161_M	0.516	1.00
197_T	210_D	0.516	1.00
204_R	356_D	0.514	1.00
70_L	298_F	0.514	1.00
370_V	374_L	0.514	1.00
260_F	263_E	0.513	1.00
141_T	170_V	0.513	1.00
24_F	83_T	0.506	1.00
188_D	194_I	0.506	1.00
110_F	113_K	0.506	1.00
90_H	114_E	0.506	1.00
184_L	224_V	0.504	1.00
50_Y	72_F	0.504	1.00
123_R	171_T	0.503	1.00
69_M	92_S	0.502	1.00
194_I	209_H	0.502	1.00
240_L	297_L	0.500	1.00
273_I	279_V	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
3pfdA	4	0.9528	100	0.097	Contact Map
4w9uA	4	0.9554	100	0.098	Contact Map
2d29A	4	0.9816	100	0.1	Contact Map
3ii9A	4	0.979	100	0.101	Contact Map
4l1fA	4	0.979	100	0.101	Contact Map
1bucA	4	0.9764	100	0.104	Contact Map
2ebaA	4	0.9659	100	0.104	Contact Map
2jifA	4	0.979	100	0.107	Contact Map
3nf4A	4	0.9711	100	0.108	Contact Map
1ivhA	4	0.9816	100	0.108	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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