DACD - ECOLI - GREMLIN Contacts

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DACD - D-alanyl-D-alanine carboxypeptidase DacD

UniProt:	P33013	Sequences: MKRRLIIAASLFVFNLSSGFAAENIPFSPQPPEIHAGSWVLMDYTTGQILTAGNEHQQRNPASLTKLMTGYVVDRAIDSHRITPDDIVTVGRDAWAKDNPVFVGSSLMFLKEGDRVSVRDLSRGLIVDSGNDACVALADYIAGGQRQFVEMMNNYAEKLHLKDTHFETVHGLDAPGQHSSAYDLAVLSRAIIHGEPEFYHMYSEKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQRRLIAVVMGADSAKGREEEARKLLRWGQQNFTTVQILHRGKKVGTERIWYGDKENIDLGTEQEFWMVLPKAEIPHIKAKYTLDGKELTAPISAHQRVGEIELYDRDKQVAHWPLVTLESVGEGSMFSRLSDYFHHKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11893
Length:	388 (364)
Sequences:	4218 (3357)
Seq/√Len:	176.0

ECOLI - DACD DACC DACA PBP7
BACSU - DACF DACA DACB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_H	182_Y	3.770	1.00
52_A	55_E	3.741	1.00
118_V	137_L	3.037	1.00
142_A	151_M	2.959	1.00
91_G	139_D	2.899	1.00
87_I	115_R	2.887	1.00
73_V	137_L	2.818	1.00
350_E	362_H	2.745	1.00
41_L	278_G	2.674	1.00
54_N	57_Q	2.621	1.00
229_D	253_R	2.547	1.00
188_S	231_L	2.529	1.00
92_R	112_E	2.485	1.00
161_L	187_L	2.481	1.00
254_L	278_G	2.477	1.00
86_D	140_Y	2.462	1.00
347_R	364_P	2.417	1.00
123_R	204_E	2.400	1.00
155_Y	158_K	2.393	1.00
125_L	137_L	2.378	1.00
227_N	249_D	2.377	1.00
58_Q	178_H	2.349	1.00
75_R	155_Y	2.338	1.00
71_Y	190_A	2.326	1.00
229_D	246_S	2.262	1.00
67_L	244_I	2.206	1.00
117_S	120_D	2.172	1.00
56_H	163_D	2.163	1.00
124_G	130_G	2.161	1.00
248_V	251_Q	2.114	1.00
125_L	134_C	2.096	1.00
342_I	367_T	2.080	1.00
68_M	164_T	2.037	1.00
39_W	51_T	2.033	1.00
145_Q	169_V	1.991	1.00
44_Y	255_I	1.978	1.00
147_Q	150_E	1.974	1.00
304_K	369_E	1.962	1.00
182_Y	186_V	1.958	1.00
286_Q	289_H	1.956	1.00
89_T	115_R	1.942	1.00
83_T	86_D	1.937	1.00
256_A	271_A	1.912	1.00
144_G	147_Q	1.866	1.00
310_G	368_L	1.851	1.00
68_M	156_A	1.812	1.00
58_Q	163_D	1.811	1.00
354_Y	359_Q	1.800	1.00
338_L	348_V	1.794	1.00
188_S	244_I	1.746	1.00
82_I	118_V	1.744	1.00
270_E	273_K	1.741	1.00
247_A	279_Q	1.733	1.00
150_E	154_N	1.728	1.00
159_L	190_A	1.690	1.00
87_I	117_S	1.686	1.00
88_V	140_Y	1.684	1.00
142_A	147_Q	1.668	1.00
92_R	96_A	1.648	1.00
347_R	350_E	1.644	1.00
38_S	59_R	1.640	1.00
41_L	254_L	1.633	1.00
197_E	200_H	1.630	1.00
90_V	136_A	1.628	1.00
93_D	139_D	1.622	1.00
88_V	136_A	1.620	1.00
70_G	126_I	1.612	1.00
38_S	181_A	1.612	1.00
346_Q	367_T	1.610	1.00
64_L	244_I	1.594	1.00
330_K	354_Y	1.593	1.00
91_G	94_A	1.584	1.00
64_L	184_L	1.583	1.00
85_D	119_R	1.577	1.00
161_L	186_V	1.562	1.00
359_Q	362_H	1.562	1.00
190_A	193_H	1.543	1.00
70_G	125_L	1.542	1.00
312_E	364_P	1.538	1.00
43_D	252_R	1.536	1.00
164_T	179_S	1.531	1.00
348_V	367_T	1.529	1.00
82_I	140_Y	1.515	1.00
236_T	239_A	1.504	1.00
296_T	306_N	1.504	1.00
69_T	134_C	1.504	1.00
165_H	178_H	1.502	1.00
154_N	158_K	1.493	1.00
189_R	255_I	1.493	1.00
73_V	118_V	1.473	1.00
127_V	204_E	1.470	1.00
37_G	260_G	1.461	1.00
225_T	276_R	1.437	1.00
352_E	362_H	1.434	1.00
181_A	259_M	1.428	1.00
173_D	238_G	1.427	1.00
119_R	123_R	1.425	1.00
76_A	81_R	1.411	1.00
119_R	200_H	1.406	1.00
167_E	176_G	1.402	1.00
343_S	370_S	1.398	1.00
332_T	352_E	1.396	1.00
206_S	213_T	1.394	1.00
307_I	367_T	1.376	1.00
70_G	122_S	1.370	1.00
343_S	346_Q	1.355	1.00
344_A	370_S	1.355	1.00
61_P	179_S	1.352	1.00
119_R	201_M	1.352	1.00
40_V	55_E	1.351	1.00
352_E	359_Q	1.339	1.00
65_T	177_Q	1.331	1.00
40_V	182_Y	1.320	1.00
90_V	110_L	1.319	1.00
123_R	207_L	1.316	1.00
124_G	133_A	1.311	1.00
84_P	122_S	1.297	1.00
190_A	194_G	1.295	1.00
184_L	244_I	1.291	1.00
167_E	174_A	1.285	1.00
286_Q	316_W	1.277	1.00
228_V	245_A	1.265	1.00
60_N	173_D	1.264	1.00
156_A	161_L	1.243	1.00
208_T	213_T	1.241	1.00
330_K	352_E	1.237	1.00
64_L	259_M	1.230	1.00
245_A	271_A	1.229	1.00
84_P	119_R	1.228	1.00
123_R	127_V	1.221	1.00
151_M	154_N	1.221	1.00
94_A	139_D	1.215	1.00
189_R	193_H	1.215	1.00
60_N	238_G	1.209	1.00
248_V	253_R	1.208	1.00
41_L	256_A	1.208	1.00
199_Y	246_S	1.207	1.00
246_S	253_R	1.207	1.00
332_T	350_E	1.203	1.00
71_Y	155_Y	1.196	1.00
147_Q	151_M	1.174	1.00
78_D	197_E	1.174	1.00
331_Y	365_L	1.173	1.00
73_V	125_L	1.165	1.00
108_M	124_G	1.165	1.00
205_K	222_W	1.163	1.00
38_S	54_N	1.152	1.00
367_T	370_S	1.149	1.00
71_Y	194_G	1.137	1.00
308_D	368_L	1.137	1.00
76_A	151_M	1.130	1.00
283_T	321_K	1.128	1.00
374_G	378_S	1.127	1.00
129_S	232_K	1.127	1.00
55_E	182_Y	1.123	1.00
42_M	185_A	1.120	1.00
40_V	49_I	1.117	1.00
67_L	231_L	1.116	1.00
82_I	137_L	1.106	1.00
155_Y	190_A	1.097	1.00
323_E	326_H	1.094	1.00
103_V	135_V	1.090	1.00
72_V	76_A	1.090	1.00
263_S	266_G	1.089	1.00
239_A	242_N	1.089	1.00
67_L	188_S	1.086	1.00
303_D	372_G	1.081	1.00
77_I	198_F	1.078	1.00
39_W	53_G	1.065	1.00
296_T	308_D	1.065	1.00
261_A	270_E	1.063	1.00
302_G	340_A	1.062	1.00
56_H	180_S	1.058	1.00
289_H	314_E	1.056	1.00
258_V	271_A	1.055	1.00
225_T	228_V	1.047	1.00
47_G	189_R	1.043	1.00
202_Y	231_L	1.041	1.00
286_Q	314_E	1.039	0.99
167_E	177_Q	1.038	0.99
149_V	169_V	1.030	0.99
309_L	348_V	1.029	0.99
247_A	275_L	1.028	0.99
272_R	276_R	1.028	0.99
73_V	82_I	1.020	0.99
149_V	153_N	1.015	0.99
156_A	187_L	1.009	0.99
36_A	261_A	1.008	0.99
90_V	116_V	1.006	0.99
192_I	199_Y	1.003	0.99
312_E	366_V	0.997	0.99
289_H	292_K	0.992	0.99
375_S	378_S	0.992	0.99
134_C	169_V	0.991	0.99
290_R	314_E	0.991	0.99
328_K	354_Y	0.990	0.99
77_I	82_I	0.989	0.99
199_Y	253_R	0.985	0.99
58_Q	180_S	0.984	0.99
249_D	279_Q	0.983	0.99
93_D	146_R	0.979	0.99
228_V	275_L	0.976	0.99
245_A	275_L	0.972	0.99
72_V	155_Y	0.964	0.99
95_W	112_E	0.964	0.99
129_S	233_T	0.964	0.99
13_V	16_L	0.956	0.99
185_A	257_V	0.954	0.99
163_D	180_S	0.950	0.99
85_D	117_S	0.946	0.99
354_Y	357_D	0.946	0.99
72_V	141_I	0.937	0.99
76_A	141_I	0.934	0.99
43_D	284_T	0.934	0.99
249_D	276_R	0.928	0.99
37_G	59_R	0.927	0.99
225_T	247_A	0.926	0.99
307_I	371_V	0.923	0.99
45_T	284_T	0.923	0.99
141_I	151_M	0.923	0.99
61_P	259_M	0.921	0.99
297_E	309_L	0.919	0.99
74_D	198_F	0.918	0.99
288_L	311_T	0.917	0.99
299_I	302_G	0.916	0.99
374_G	382_D	0.914	0.99
244_I	257_V	0.909	0.99
165_H	176_G	0.906	0.99
299_I	340_A	0.905	0.99
277_W	282_F	0.902	0.99
162_K	182_Y	0.897	0.99
308_D	369_E	0.896	0.98
93_D	145_Q	0.892	0.98
373_E	379_R	0.881	0.98
231_L	246_S	0.876	0.98
184_L	259_M	0.874	0.98
135_V	145_Q	0.872	0.98
88_V	118_V	0.871	0.98
73_V	141_I	0.866	0.98
45_T	316_W	0.865	0.98
35_H	270_E	0.865	0.98
200_H	203_S	0.865	0.98
130_G	133_A	0.861	0.98
110_L	136_A	0.861	0.98
284_T	318_V	0.859	0.98
111_K	114_D	0.857	0.98
67_L	191_I	0.857	0.98
40_V	52_A	0.856	0.98
225_T	272_R	0.855	0.98
126_I	202_Y	0.849	0.98
63_S	232_K	0.848	0.98
307_I	342_I	0.848	0.98
179_S	184_L	0.845	0.98
45_T	253_R	0.845	0.98
90_V	121_L	0.844	0.98
43_D	318_V	0.841	0.98
10_S	16_L	0.840	0.98
14_F	17_S	0.840	0.98
77_I	84_P	0.835	0.98
40_V	257_V	0.833	0.98
191_I	231_L	0.831	0.98
75_R	194_G	0.829	0.98
315_F	361_A	0.829	0.98
62_A	239_A	0.828	0.97
68_M	152_M	0.826	0.97
173_D	236_T	0.825	0.97
277_W	281_N	0.822	0.97
33_E	53_G	0.822	0.97
248_V	279_Q	0.822	0.97
153_N	165_H	0.819	0.97
342_I	348_V	0.819	0.97
284_T	316_W	0.818	0.97
346_Q	370_S	0.817	0.97
186_V	189_R	0.816	0.97
154_N	157_E	0.814	0.97
209_W	214_Q	0.812	0.97
285_V	324_I	0.810	0.97
199_Y	202_Y	0.807	0.97
329_A	353_L	0.806	0.97
84_P	201_M	0.805	0.97
42_M	189_R	0.804	0.97
121_L	133_A	0.804	0.97
120_D	123_R	0.803	0.97
227_N	276_R	0.799	0.97
116_V	121_L	0.798	0.97
351_I	363_W	0.796	0.97
198_F	202_Y	0.789	0.97
116_V	120_D	0.789	0.97
40_V	185_A	0.789	0.97
341_P	371_V	0.788	0.97
184_L	188_S	0.787	0.97
67_L	126_I	0.783	0.96
157_E	162_K	0.781	0.96
243_L	271_A	0.780	0.96
256_A	275_L	0.778	0.96
338_L	342_I	0.775	0.96
258_V	261_A	0.774	0.96
206_S	215_Q	0.773	0.96
262_D	266_G	0.773	0.96
82_I	88_V	0.772	0.96
89_T	140_Y	0.770	0.96
315_F	363_W	0.769	0.96
38_S	259_M	0.767	0.96
78_D	194_G	0.766	0.96
75_R	79_S	0.766	0.96
72_V	75_R	0.764	0.96
76_A	82_I	0.764	0.96
207_L	214_Q	0.763	0.96
120_D	210_N	0.757	0.96
50_L	282_F	0.756	0.96
188_S	230_G	0.754	0.96
116_V	209_W	0.753	0.96
214_Q	217_R	0.753	0.96
152_M	156_A	0.753	0.96
106_S	130_G	0.751	0.96
235_H	241_F	0.751	0.96
166_F	184_L	0.749	0.95
156_A	166_F	0.749	0.95
82_I	86_D	0.747	0.95
219_G	268_E	0.740	0.95
153_N	166_F	0.740	0.95
236_T	242_N	0.740	0.95
146_R	150_E	0.739	0.95
156_A	159_L	0.738	0.95
192_I	229_D	0.736	0.95
68_M	72_V	0.735	0.95
103_V	107_L	0.734	0.95
114_D	212_I	0.732	0.95
91_G	136_A	0.731	0.95
302_G	371_V	0.730	0.95
218_N	245_A	0.725	0.95
122_S	201_M	0.723	0.95
326_H	356_R	0.722	0.94
218_N	243_L	0.722	0.94
37_G	57_Q	0.721	0.94
63_S	234_G	0.719	0.94
107_L	110_L	0.717	0.94
84_P	87_I	0.716	0.94
74_D	122_S	0.716	0.94
68_M	166_F	0.716	0.94
256_A	274_L	0.714	0.94
311_T	365_L	0.712	0.94
302_G	341_P	0.710	0.94
123_R	201_M	0.708	0.94
18_S	23_E	0.704	0.94
20_F	23_E	0.702	0.94
68_M	161_L	0.702	0.94
128_D	217_R	0.702	0.94
70_G	74_D	0.698	0.93
48_Q	318_V	0.698	0.93
192_I	253_R	0.694	0.93
376_M	380_L	0.690	0.93
191_I	198_F	0.688	0.93
355_D	358_K	0.687	0.93
159_L	187_L	0.683	0.93
345_H	367_T	0.681	0.93
60_N	174_A	0.677	0.92
63_S	129_S	0.674	0.92
80_H	83_T	0.672	0.92
64_L	242_N	0.672	0.92
108_M	128_D	0.671	0.92
18_S	22_A	0.671	0.92
72_V	152_M	0.669	0.92
252_R	284_T	0.668	0.92
63_S	66_K	0.668	0.92
88_V	121_L	0.668	0.92
225_T	275_L	0.667	0.92
293_K	308_D	0.666	0.92
327_I	355_D	0.665	0.92
108_M	116_V	0.663	0.92
128_D	214_Q	0.659	0.91
70_G	202_Y	0.658	0.91
329_A	351_I	0.658	0.91
151_M	155_Y	0.657	0.91
273_K	276_R	0.656	0.91
252_R	282_F	0.655	0.91
105_S	109_F	0.654	0.91
21_A	25_I	0.652	0.91
104_G	107_L	0.652	0.91
309_L	365_L	0.651	0.91
76_A	79_S	0.651	0.91
202_Y	230_G	0.651	0.91
266_G	270_E	0.649	0.91
320_P	323_E	0.647	0.91
59_R	259_M	0.647	0.91
208_T	211_G	0.644	0.90
68_M	187_L	0.643	0.90
75_R	158_K	0.642	0.90
355_D	360_V	0.641	0.90
227_N	247_A	0.636	0.90
67_L	187_L	0.634	0.90
327_I	360_V	0.634	0.90
245_A	256_A	0.633	0.90
105_S	132_D	0.633	0.90
163_D	183_D	0.631	0.90
42_M	255_I	0.629	0.89
261_A	266_G	0.628	0.89
120_D	207_L	0.628	0.89
126_I	198_F	0.625	0.89
21_A	24_N	0.624	0.89
184_L	242_N	0.623	0.89
202_Y	246_S	0.615	0.88
162_K	186_V	0.614	0.88
121_L	137_L	0.614	0.88
198_F	231_L	0.613	0.88
217_R	235_H	0.613	0.88
52_A	182_Y	0.610	0.88
165_H	177_Q	0.610	0.88
311_T	315_F	0.610	0.88
164_T	183_D	0.610	0.88
32_P	277_W	0.609	0.88
161_L	183_D	0.608	0.88
149_V	164_T	0.607	0.88
18_S	21_A	0.606	0.88
334_D	337_E	0.606	0.88
63_S	233_T	0.605	0.87
378_S	381_S	0.603	0.87
127_V	207_L	0.603	0.87
155_Y	159_L	0.602	0.87
44_Y	253_R	0.601	0.87
81_R	151_M	0.599	0.87
20_F	24_N	0.596	0.87
62_A	233_T	0.596	0.87
12_F	16_L	0.594	0.87
72_V	151_M	0.594	0.87
350_E	364_P	0.592	0.86
228_V	247_A	0.591	0.86
331_Y	351_I	0.591	0.86
62_A	65_T	0.591	0.86
82_I	141_I	0.590	0.86
65_T	179_S	0.590	0.86
34_I	39_W	0.589	0.86
258_V	274_L	0.589	0.86
127_V	201_M	0.586	0.86
285_V	319_L	0.585	0.86
74_D	197_E	0.584	0.86
153_N	157_E	0.582	0.85
42_M	186_V	0.582	0.85
179_S	183_D	0.581	0.85
300_W	337_E	0.581	0.85
19_G	22_A	0.581	0.85
141_I	149_V	0.581	0.85
192_I	231_L	0.579	0.85
275_L	278_G	0.579	0.85
66_K	131_N	0.579	0.85
303_D	378_S	0.578	0.85
106_S	233_T	0.577	0.85
19_G	23_E	0.576	0.85
191_I	202_Y	0.575	0.85
61_P	177_Q	0.574	0.85
340_A	371_V	0.572	0.84
218_N	221_L	0.572	0.84
48_Q	358_K	0.571	0.84
274_L	278_G	0.571	0.84
138_A	145_Q	0.569	0.84
64_L	67_L	0.569	0.84
61_P	65_T	0.568	0.84
243_L	256_A	0.567	0.84
43_D	46_T	0.565	0.84
291_G	311_T	0.565	0.84
243_L	258_V	0.564	0.84
52_A	56_H	0.563	0.83
49_I	55_E	0.563	0.83
72_V	164_T	0.561	0.83
114_D	210_N	0.561	0.83
62_A	129_S	0.561	0.83
124_G	209_W	0.561	0.83
293_K	296_T	0.560	0.83
173_D	239_A	0.560	0.83
25_I	28_S	0.555	0.83
301_Y	339_T	0.553	0.82
233_T	267_R	0.552	0.82
136_A	140_Y	0.552	0.82
12_F	15_N	0.551	0.82
74_D	201_M	0.551	0.82
229_D	248_V	0.551	0.82
378_S	382_D	0.549	0.82
170_H	173_D	0.548	0.82
116_V	124_G	0.548	0.82
75_R	78_D	0.548	0.82
225_T	249_D	0.547	0.82
36_A	270_E	0.545	0.81
288_L	351_I	0.545	0.81
108_M	130_G	0.545	0.81
243_L	268_E	0.545	0.81
225_T	279_Q	0.545	0.81
44_Y	189_R	0.545	0.81
288_L	353_L	0.545	0.81
49_I	52_A	0.544	0.81
235_H	264_A	0.543	0.81
281_N	320_P	0.541	0.81
241_F	267_R	0.541	0.81
107_L	132_D	0.541	0.81
16_L	20_F	0.540	0.81
71_Y	159_L	0.540	0.81
319_L	327_I	0.539	0.81
10_S	13_V	0.539	0.81
224_K	272_R	0.538	0.81
203_S	229_D	0.537	0.81
42_M	49_I	0.536	0.80
58_Q	179_S	0.536	0.80
103_V	172_L	0.534	0.80
196_P	199_Y	0.534	0.80
50_L	254_L	0.534	0.80
11_L	15_N	0.532	0.80
18_S	24_N	0.532	0.80
184_L	187_L	0.532	0.80
145_Q	149_V	0.532	0.80
41_L	274_L	0.529	0.80
93_D	135_V	0.528	0.79
287_I	317_M	0.526	0.79
62_A	234_G	0.526	0.79
119_R	197_E	0.525	0.79
51_T	274_L	0.524	0.79
16_L	19_G	0.523	0.79
90_V	114_D	0.523	0.79
106_S	232_K	0.522	0.79
20_F	25_I	0.519	0.78
328_K	357_D	0.519	0.78
254_L	279_Q	0.517	0.78
74_D	202_Y	0.517	0.78
108_M	214_Q	0.516	0.78
359_Q	363_W	0.516	0.78
199_Y	229_D	0.514	0.78
199_Y	203_S	0.512	0.77
377_F	381_S	0.512	0.77
54_N	59_R	0.511	0.77
42_M	47_G	0.510	0.77
263_S	267_R	0.510	0.77
186_V	190_A	0.510	0.77
71_Y	187_L	0.509	0.77
142_A	145_Q	0.508	0.77
67_L	74_D	0.508	0.77
110_L	116_V	0.508	0.77
148_F	152_M	0.507	0.77
124_G	214_Q	0.507	0.77
34_I	270_E	0.506	0.77
61_P	184_L	0.506	0.77
177_Q	242_N	0.505	0.76
219_G	264_A	0.505	0.76
345_H	366_V	0.503	0.76
287_I	353_L	0.502	0.76
241_F	268_E	0.501	0.76
92_R	95_W	0.501	0.76
205_K	215_Q	0.501	0.76
22_A	26_P	0.500	0.76

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
3mzfA	1	0.9046	100	0.228	Contact Map
4k91A	1	0.884	100	0.246	Contact Map
3itaA	1	0.8969	100	0.247	Contact Map
3a3jA	1	0.8789	100	0.261	Contact Map
1xp4A	3	0.8686	100	0.268	Contact Map
3mfdA	1	0.8222	100	0.279	Contact Map
3hunA	1	0.8222	100	0.365	Contact Map
1tvfA	1	0.8608	100	0.393	Contact Map
4pprA	1	0.7371	100	0.477	Contact Map
4ryeA	1	0.6572	100	0.486	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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