YGIC - ECOLI - GREMLIN Contacts

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YGIC - Putative acid--amine ligase YgiC

UniProt:	P0ADT5	Sequences: MERVSITERPDWREKAHEYGFNFHTMYGEPYWCEDAYYKLTLAQVEKLEEVTAELHQMCLKVVEKVIASDELMTKFRIPKHTWSFVRQSWLTHQPSLYSRLDLAWDGTGEPKLLENNADTPTSLYEAAFFQWIWLEDQLNAGNLPEGSDQFNSLQEKLIDRFVELREQYGFQLLHLTCCRDTVEDRGTIQYLQDCATEAEIATEFLYIDDIGLGEKGQFTDLQDQVISNLFKLYPWEFMLREMFSTKLEDAGVRWLEPAWKSIISNKALLPLLWEMFPNHPNLLPAYFAEDDHPQMEKYVVKPIFSREGANVSIIENGKTIEAAEGPYGEEGMIVQQFHPLPKFGDSYMLIGSWLVNDQPAGIGIREDRALITQDMSRFYPHIFVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11165
Length:	386 (364)
Sequences:	1265 (866)
Seq/√Len:	45.4

ECOLI - YGIC YJFC GSP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_A	360_P	5.430	1.00
52_T	353_S	5.264	1.00
99_S	116_N	4.107	1.00
343_K	346_D	4.083	1.00
65_K	276_M	3.939	1.00
314_I	338_F	3.695	1.00
42_L	46_E	3.282	1.00
64_E	68_A	3.252	1.00
56_H	116_N	3.246	1.00
311_N	326_G	3.016	1.00
300_V	314_I	2.892	1.00
74_T	83_W	2.722	1.00
51_V	111_P	2.605	1.00
106_D	109_G	2.576	1.00
65_K	69_S	2.534	1.00
76_F	268_A	2.532	1.00
43_A	47_K	2.521	1.00
15_K	18_E	2.430	1.00
40_L	45_V	2.415	1.00
177_T	208_I	2.379	1.00
27_Y	376_M	2.301	1.00
259_A	262_S	2.295	1.00
218_Q	226_V	2.290	1.00
285_P	289_A	2.289	1.00
153_S	157_K	2.278	1.00
301_V	313_S	2.272	1.00
26_M	376_M	2.223	1.00
211_I	227_I	2.204	1.00
127_A	154_L	2.189	1.00
14_E	17_H	2.109	1.00
175_H	206_L	2.095	1.00
17_H	24_H	2.093	1.00
74_T	80_K	2.071	0.99
157_K	361_A	2.064	0.99
257_E	265_S	2.050	0.99
73_M	87_R	2.036	0.99
190_Q	193_Q	2.030	0.99
62_V	276_M	1.963	0.99
271_P	288_F	1.930	0.99
73_M	83_W	1.916	0.99
288_F	291_D	1.889	0.99
178_C	205_F	1.886	0.99
55_L	101_L	1.883	0.99
62_V	272_L	1.870	0.99
72_L	275_E	1.848	0.99
289_A	294_P	1.827	0.99
37_Y	383_I	1.817	0.99
66_V	72_L	1.780	0.98
271_P	334_I	1.770	0.98
193_Q	203_T	1.756	0.98
368_D	374_Q	1.746	0.98
66_V	263_I	1.741	0.98
193_Q	197_T	1.727	0.98
207_Y	210_D	1.726	0.98
180_R	209_D	1.724	0.98
114_L	341_L	1.699	0.98
351_I	365_I	1.688	0.98
176_L	192_L	1.685	0.98
173_L	202_A	1.676	0.98
206_L	222_L	1.648	0.97
237_E	307_R	1.630	0.97
159_I	195_C	1.610	0.97
15_K	137_D	1.599	0.97
343_K	348_Y	1.570	0.96
14_E	18_E	1.556	0.96
70_D	73_M	1.546	0.96
299_Y	315_I	1.537	0.96
86_V	259_A	1.533	0.96
267_K	302_K	1.532	0.96
159_I	198_E	1.531	0.96
23_F	188_T	1.530	0.96
48_L	363_I	1.530	0.96
16_A	21_F	1.513	0.96
197_T	202_A	1.505	0.96
235_P	307_R	1.497	0.95
297_E	337_Q	1.490	0.95
240_L	262_S	1.485	0.95
270_L	286_A	1.477	0.95
52_T	355_L	1.467	0.95
284_L	289_A	1.467	0.95
202_A	225_Q	1.464	0.95
115_E	302_K	1.457	0.95
329_G	332_G	1.455	0.95
351_I	363_I	1.451	0.95
105_W	111_P	1.437	0.94
178_C	207_Y	1.435	0.94
15_K	19_Y	1.433	0.94
62_V	269_L	1.431	0.94
286_A	290_E	1.417	0.94
101_L	113_L	1.411	0.94
300_V	312_V	1.407	0.94
42_L	384_F	1.397	0.93
61_K	277_F	1.391	0.93
174_L	201_I	1.382	0.93
102_D	302_K	1.380	0.93
33_C	378_R	1.376	0.93
113_L	270_L	1.371	0.93
230_L	255_W	1.368	0.93
210_D	222_L	1.367	0.93
213_L	247_K	1.366	0.93
122_T	233_L	1.361	0.92
320_T	323_A	1.351	0.92
180_R	207_Y	1.348	0.92
214_G	220_T	1.336	0.92
63_V	264_I	1.326	0.91
104_A	114_L	1.326	0.91
102_D	267_K	1.314	0.91
27_Y	374_Q	1.312	0.91
175_H	227_I	1.306	0.91
115_E	267_K	1.299	0.90
298_K	337_Q	1.292	0.90
291_D	294_P	1.286	0.90
101_L	355_L	1.285	0.90
204_E	225_Q	1.275	0.90
175_H	204_E	1.264	0.89
301_V	335_V	1.259	0.89
164_E	357_N	1.255	0.89
26_M	374_Q	1.244	0.88
177_T	230_L	1.239	0.88
161_R	165_L	1.219	0.87
301_V	333_M	1.217	0.87
220_T	224_D	1.206	0.87
52_T	103_L	1.206	0.87
59_C	118_A	1.205	0.87
102_D	336_Q	1.205	0.87
289_A	292_D	1.203	0.87
162_F	195_C	1.201	0.87
193_Q	205_F	1.191	0.86
62_V	65_K	1.191	0.86
51_V	282_N	1.189	0.86
102_D	115_E	1.182	0.86
56_H	355_L	1.181	0.86
204_E	223_Q	1.179	0.86
87_R	91_L	1.175	0.85
69_S	74_T	1.174	0.85
160_D	164_E	1.172	0.85
354_W	367_E	1.171	0.85
268_A	304_I	1.166	0.85
285_P	337_Q	1.162	0.85
121_P	257_E	1.161	0.85
298_K	316_E	1.159	0.85
272_L	276_M	1.158	0.85
350_L	373_T	1.157	0.85
232_K	236_W	1.151	0.84
114_L	339_H	1.141	0.84
181_D	209_D	1.140	0.84
70_D	87_R	1.133	0.83
84_S	88_Q	1.128	0.83
72_L	75_K	1.125	0.83
100_R	362_G	1.122	0.83
83_W	87_R	1.120	0.83
122_T	308_E	1.119	0.82
176_L	193_Q	1.119	0.82
64_E	295_Q	1.118	0.82
274_W	280_H	1.106	0.82
322_E	371_L	1.092	0.81
257_E	261_K	1.090	0.81
31_Y	373_T	1.078	0.80
254_R	287_Y	1.075	0.80
302_K	336_Q	1.070	0.80
98_Y	231_F	1.069	0.79
154_L	362_G	1.059	0.79
100_R	352_G	1.058	0.79
120_T	308_E	1.057	0.79
267_K	336_Q	1.054	0.78
184_E	307_R	1.043	0.78
29_E	52_T	1.038	0.77
22_N	26_M	1.037	0.77
157_K	359_Q	1.037	0.77
238_F	383_I	1.029	0.77
158_L	162_F	1.023	0.76
285_P	288_F	1.021	0.76
173_L	228_S	1.021	0.76
246_T	250_D	1.011	0.76
19_Y	137_D	1.010	0.75
38_Y	367_E	1.007	0.75
348_Y	370_A	1.005	0.75
58_M	277_F	0.997	0.74
25_T	29_E	0.992	0.74
227_I	230_L	0.989	0.74
233_L	307_R	0.986	0.74
316_E	319_K	0.980	0.73
117_N	267_K	0.974	0.73
368_D	377_S	0.970	0.72
214_G	218_Q	0.970	0.72
88_Q	92_T	0.970	0.72
311_N	325_E	0.968	0.72
78_I	263_I	0.964	0.72
120_T	126_E	0.962	0.72
175_H	221_D	0.960	0.72
103_L	113_L	0.956	0.71
120_T	257_E	0.956	0.71
189_I	205_F	0.955	0.71
315_I	320_T	0.955	0.71
179_C	209_D	0.955	0.71
227_I	253_V	0.954	0.71
119_D	232_K	0.949	0.71
119_D	122_T	0.947	0.71
197_T	323_A	0.947	0.71
85_F	259_A	0.945	0.70
374_Q	377_S	0.944	0.70
149_D	384_F	0.944	0.70
185_D	188_T	0.943	0.70
230_L	259_A	0.942	0.70
248_L	255_W	0.941	0.70
53_A	359_Q	0.940	0.70
21_F	125_Y	0.939	0.70
48_L	353_S	0.933	0.69
377_S	382_H	0.932	0.69
119_D	237_E	0.930	0.69
126_E	307_R	0.930	0.69
58_M	210_D	0.929	0.69
284_L	290_E	0.927	0.69
174_L	229_N	0.917	0.68
204_E	221_D	0.914	0.68
41_T	44_Q	0.914	0.68
296_M	315_I	0.913	0.68
77_R	332_G	0.910	0.68
286_A	289_A	0.909	0.67
55_L	283_L	0.908	0.67
262_S	305_F	0.904	0.67
186_R	205_F	0.903	0.67
115_E	336_Q	0.901	0.67
313_S	320_T	0.898	0.66
285_P	291_D	0.897	0.66
101_L	116_N	0.896	0.66
166_R	243_M	0.896	0.66
206_L	210_D	0.895	0.66
53_A	57_Q	0.894	0.66
230_L	253_V	0.893	0.66
176_L	189_I	0.891	0.66
302_K	309_G	0.885	0.65
316_E	340_P	0.881	0.65
47_K	50_E	0.879	0.65
172_Q	228_S	0.876	0.65
21_F	26_M	0.875	0.64
161_R	357_N	0.872	0.64
75_K	290_E	0.871	0.64
117_N	302_K	0.867	0.64
84_S	295_Q	0.865	0.64
230_L	239_M	0.861	0.63
285_P	290_E	0.860	0.63
247_K	250_D	0.858	0.63
235_P	308_E	0.858	0.63
364_G	379_F	0.854	0.63
347_S	378_R	0.850	0.62
353_S	360_P	0.849	0.62
112_K	337_Q	0.849	0.62
127_A	365_I	0.844	0.62
265_S	307_R	0.843	0.62
56_H	101_L	0.842	0.61
185_D	307_R	0.840	0.61
104_A	339_H	0.835	0.61
149_D	153_S	0.834	0.61
56_H	358_D	0.833	0.61
28_G	376_M	0.833	0.61
82_T	240_L	0.832	0.60
197_T	203_T	0.831	0.60
165_L	256_L	0.830	0.60
119_D	126_E	0.830	0.60
186_R	345_G	0.828	0.60
14_E	216_K	0.827	0.60
26_M	154_L	0.824	0.60
59_C	264_I	0.824	0.60
300_V	338_F	0.823	0.60
286_A	291_D	0.823	0.60
184_E	237_E	0.822	0.60
269_L	303_P	0.813	0.59
322_E	325_E	0.812	0.59
236_W	255_W	0.812	0.59
94_Q	259_A	0.808	0.58
342_P	349_M	0.800	0.57
284_L	288_F	0.796	0.57
81_H	84_S	0.796	0.57
46_E	384_F	0.787	0.56
21_F	187_G	0.785	0.56
123_S	364_G	0.784	0.56
194_D	198_E	0.783	0.56
22_N	183_V	0.782	0.56
120_T	185_D	0.780	0.56
126_E	184_E	0.778	0.55
103_L	177_T	0.772	0.55
196_A	280_H	0.769	0.54
218_Q	228_S	0.768	0.54
17_H	25_T	0.768	0.54
275_E	324_A	0.767	0.54
178_C	181_D	0.765	0.54
100_R	302_K	0.764	0.54
89_S	260_W	0.763	0.54
233_L	308_E	0.759	0.54
164_E	197_T	0.758	0.53
126_E	257_E	0.757	0.53
126_E	352_G	0.756	0.53
190_Q	197_T	0.755	0.53
74_T	77_R	0.753	0.53
72_L	79_P	0.746	0.52
104_A	113_L	0.738	0.51
174_L	227_I	0.737	0.51
234_Y	238_F	0.735	0.51
99_S	355_L	0.735	0.51
62_V	277_F	0.733	0.51
115_E	309_G	0.732	0.51
101_L	357_N	0.732	0.51
290_E	293_H	0.732	0.51
251_A	255_W	0.730	0.51
24_H	28_G	0.729	0.51
206_L	227_I	0.729	0.51
16_A	125_Y	0.728	0.50
121_P	308_E	0.728	0.50
154_L	349_M	0.728	0.50
227_I	318_G	0.725	0.50
58_M	283_L	0.723	0.50
297_E	334_I	0.722	0.50
319_K	355_L	0.722	0.50
17_H	109_G	0.721	0.50
202_A	359_Q	0.720	0.50
31_Y	34_E	0.720	0.50
96_S	373_T	0.720	0.50
317_N	320_T	0.719	0.50
247_K	252_G	0.718	0.50
206_L	223_Q	0.717	0.49
185_D	235_P	0.717	0.49
149_D	152_N	0.717	0.49
118_A	264_I	0.716	0.49
15_K	30_P	0.715	0.49
161_R	164_E	0.711	0.49
204_E	222_L	0.711	0.49
237_E	284_L	0.709	0.49
49_E	149_D	0.709	0.49
182_T	377_S	0.709	0.49
160_D	340_P	0.706	0.48
180_R	210_D	0.704	0.48
227_I	355_L	0.704	0.48
45_V	363_I	0.704	0.48
160_D	163_V	0.703	0.48
86_V	263_I	0.702	0.48
122_T	237_E	0.699	0.48
312_V	338_F	0.696	0.47
288_F	334_I	0.696	0.47
155_Q	159_I	0.694	0.47
174_L	228_S	0.694	0.47
119_D	257_E	0.693	0.47
208_I	334_I	0.692	0.47
194_D	311_N	0.691	0.47
233_L	237_E	0.690	0.47
270_L	284_L	0.689	0.47
212_G	220_T	0.689	0.47
18_E	217_G	0.688	0.47
100_R	267_K	0.685	0.46
246_T	249_E	0.684	0.46
129_F	155_Q	0.682	0.46
285_P	293_H	0.681	0.46
165_L	174_L	0.681	0.46
174_L	177_T	0.674	0.45
315_I	324_A	0.674	0.45
238_F	305_F	0.673	0.45
336_Q	366_R	0.670	0.45
178_C	189_I	0.669	0.45
60_L	264_I	0.669	0.45
102_D	117_N	0.667	0.45
98_Y	122_T	0.665	0.44
16_A	130_F	0.665	0.44
48_L	111_P	0.665	0.44
170_G	312_V	0.664	0.44
370_A	374_Q	0.662	0.44
23_F	26_M	0.661	0.44
221_D	225_Q	0.659	0.44
177_T	205_F	0.657	0.44
84_S	94_Q	0.657	0.44
176_L	205_F	0.657	0.44
154_L	157_K	0.657	0.44
152_N	158_L	0.656	0.44
152_N	156_E	0.654	0.43
295_Q	335_V	0.649	0.43
165_L	251_A	0.649	0.43
174_L	315_I	0.648	0.43
229_N	254_R	0.648	0.43
191_Y	194_D	0.647	0.43
86_V	272_L	0.646	0.43
77_R	339_H	0.645	0.42
132_W	152_N	0.645	0.42
52_T	96_S	0.639	0.42
188_T	307_R	0.638	0.42
155_Q	191_Y	0.636	0.42
348_Y	371_L	0.632	0.41
61_K	369_R	0.631	0.41
318_G	321_I	0.630	0.41
188_T	308_E	0.630	0.41
338_F	371_L	0.630	0.41
287_Y	293_H	0.629	0.41
221_D	368_D	0.628	0.41
267_K	309_G	0.621	0.40
136_E	152_N	0.619	0.40
115_E	352_G	0.619	0.40
100_R	119_D	0.614	0.40
18_E	22_N	0.613	0.39
243_M	246_T	0.611	0.39
86_V	250_D	0.611	0.39
261_K	367_E	0.611	0.39
119_D	235_P	0.605	0.39
132_W	150_Q	0.604	0.39
244_F	253_V	0.603	0.38
127_A	241_R	0.602	0.38
173_L	217_G	0.598	0.38
179_C	253_V	0.598	0.38
136_E	224_D	0.597	0.38
353_S	363_I	0.597	0.38
272_L	275_E	0.597	0.38
188_T	233_L	0.594	0.38
42_L	49_E	0.593	0.38
93_H	170_G	0.593	0.38
182_T	375_D	0.593	0.38
66_V	83_W	0.592	0.37
60_L	358_D	0.592	0.37
145_P	335_V	0.592	0.37
172_Q	202_A	0.592	0.37
149_D	194_D	0.591	0.37
320_T	324_A	0.591	0.37
45_V	49_E	0.590	0.37
119_D	233_L	0.590	0.37
133_I	263_I	0.588	0.37
258_P	270_L	0.588	0.37
191_Y	356_V	0.588	0.37
279_N	282_N	0.586	0.37
120_T	235_P	0.586	0.37
121_P	184_E	0.585	0.37
92_T	369_R	0.585	0.37
16_A	28_G	0.585	0.37
160_D	167_E	0.585	0.37
216_K	252_G	0.583	0.37
134_W	265_S	0.583	0.37
65_K	68_A	0.582	0.37
18_E	250_D	0.581	0.36
16_A	20_G	0.581	0.36
124_L	362_G	0.580	0.36
61_K	312_V	0.579	0.36
112_K	283_L	0.578	0.36
27_Y	379_F	0.577	0.36
100_R	117_N	0.577	0.36
226_V	253_V	0.577	0.36
90_W	123_S	0.577	0.36
55_L	103_L	0.576	0.36
287_Y	290_E	0.576	0.36
36_A	380_Y	0.576	0.36
199_A	281_P	0.576	0.36
220_T	226_V	0.574	0.36
227_I	303_P	0.573	0.36
118_A	122_T	0.572	0.36
284_L	292_D	0.572	0.36
40_L	365_I	0.569	0.35
84_S	249_E	0.569	0.35
227_I	372_I	0.568	0.35
14_E	19_Y	0.567	0.35
185_D	352_G	0.567	0.35
218_Q	263_I	0.566	0.35
44_Q	47_K	0.565	0.35
190_Q	198_E	0.563	0.35
138_Q	145_P	0.563	0.35
143_N	147_G	0.562	0.35
126_E	235_P	0.562	0.35
120_T	184_E	0.562	0.35
37_Y	321_I	0.559	0.35
113_L	243_M	0.556	0.34
188_T	191_Y	0.555	0.34
240_L	259_A	0.555	0.34
19_Y	22_N	0.555	0.34
178_C	253_V	0.553	0.34
92_T	251_A	0.552	0.34
163_V	166_R	0.550	0.34
96_S	109_G	0.549	0.34
235_P	305_F	0.548	0.34
287_Y	291_D	0.548	0.34
134_W	381_P	0.548	0.34
184_E	308_E	0.546	0.33
134_W	308_E	0.546	0.33
304_I	331_E	0.545	0.33
153_S	331_E	0.543	0.33
238_F	242_E	0.542	0.33
163_V	343_K	0.540	0.33
58_M	128_A	0.540	0.33
60_L	164_E	0.538	0.33
16_A	300_V	0.538	0.33
51_V	103_L	0.538	0.33
81_H	249_E	0.537	0.33
378_R	381_P	0.537	0.33
343_K	349_M	0.536	0.33
266_N	367_E	0.536	0.33
45_V	105_W	0.536	0.33
69_S	272_L	0.535	0.32
99_S	357_N	0.535	0.32
329_G	333_M	0.534	0.32
54_E	57_Q	0.532	0.32
30_P	35_D	0.531	0.32
66_V	319_K	0.529	0.32
22_N	27_Y	0.529	0.32
44_Q	63_V	0.529	0.32
265_S	303_P	0.528	0.32
55_L	293_H	0.528	0.32
131_Q	260_W	0.527	0.32
214_G	217_G	0.527	0.32
317_N	321_I	0.525	0.32
66_V	73_M	0.524	0.31
254_R	312_V	0.524	0.31
153_S	361_A	0.523	0.31
274_W	279_N	0.523	0.31
58_M	293_H	0.522	0.31
47_K	287_Y	0.521	0.31
120_T	265_S	0.521	0.31
314_I	333_M	0.520	0.31
194_D	280_H	0.520	0.31
216_K	320_T	0.519	0.31
228_S	288_F	0.519	0.31
308_E	373_T	0.519	0.31
373_T	381_P	0.518	0.31
61_K	65_K	0.518	0.31
18_E	28_G	0.517	0.31
126_E	185_D	0.515	0.31
43_A	225_Q	0.513	0.31
298_K	338_F	0.513	0.31
121_P	235_P	0.513	0.31
315_I	321_I	0.511	0.30
185_D	270_L	0.510	0.30
341_L	372_I	0.508	0.30
49_E	105_W	0.508	0.30
122_T	307_R	0.508	0.30
299_Y	317_N	0.507	0.30
192_L	233_L	0.506	0.30
64_E	93_H	0.505	0.30
115_E	366_R	0.505	0.30
43_A	53_A	0.504	0.30
14_E	41_T	0.503	0.30
86_V	90_W	0.503	0.30
69_S	72_L	0.502	0.30
188_T	231_F	0.502	0.30
166_R	201_I	0.502	0.30
126_E	232_K	0.501	0.30
98_Y	135_L	0.501	0.30
22_N	125_Y	0.501	0.30
40_L	344_F	0.501	0.30
33_C	42_L	0.500	0.30
319_K	324_A	0.500	0.30
19_Y	130_F	0.500	0.30
100_R	115_E	0.500	0.30
101_L	131_Q	0.500	0.30
223_Q	226_V	0.500	0.30
114_L	208_I	0.500	0.30

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
2vobA	1	0.8705	100	0.182	Contact Map
2io8A	2	0.9663	100	0.206	Contact Map
3n6xA	2	0.9352	100	0.467	Contact Map
2hgsA	2	0.9637	99.3	0.844	Contact Map
3kalA	2	0.9663	99.3	0.845	Contact Map
1m0wA	2	0.9715	99.3	0.847	Contact Map
1gsaA	3	0.5285	99.1	0.861	Contact Map
3vpbA	3	0.5104	98.9	0.869	Contact Map
2wyoA	2	0.9585	98.8	0.875	Contact Map
3r5xA	2	0.5233	98.8	0.875	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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