YTRF - BACSU - GREMLIN Contacts

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YTRF - ABC transporter permease YtrF

UniProt:	O35005	Sequences: MRFKDQVHFIRRNMKKNRLRVFMTILATTMACAFLVVLSSVGFGIQKTITDMTMSQQIVTKVSVMGKEGDKPIKKADLEKYDHVRSVVERTQVYEPNKATLGNRTNESSNLIFTNMNDELKANMELEKGRVAKSENEIVVGYDFAKRLLTKKESEEYNKKIEEAKGNPEDIKEPKGYTKDILNKTIELSVSKTDSKTGDVTKTKTYDFKIVGITKKPSQDWMEDSNIFISDQFKKDFSEFLDFKGGNVETNIGVFADKFENVEQLTNDLTDDGYYVTSVTTELEGANTFFMVFKIGLIFVGCIAVIISAIGIFNTMTMAVTERTQEIGIMKAIGASPSIIRRMFLMESAYIGILGCVIGIIISYGVSYLVNLAVPMILAATSGGDAGDLNYTFSYIPASLVIIAVVICGGVAVISGMNPARKATKTNVLTALRREL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	436 (363)
Sequences:	36261 (31074)
Seq/√Len:	1631.0

ECOLI - LOLC LOLE YBBP MACB
BACSU - YTRF YKNZ YVRN YCLI YXDM YVCS BCEB FTSX
HALSA - Q9HT02
SULSO - Q7LXM6 Q97XD5 Q97Z54

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
185_T	207_D	3.738	1.00
142_Y	215_K	3.598	1.00
327_I	344_F	3.418	1.00
187_E	207_D	3.385	1.00
185_T	209_K	3.366	1.00
142_Y	146_K	2.930	1.00
137_E	209_K	2.904	1.00
137_E	211_V	2.889	1.00
427_N	430_T	2.652	1.00
74_K	77_D	2.611	1.00
323_R	347_E	2.594	1.00
138_I	227_I	2.590	1.00
145_A	213_I	2.583	1.00
125_E	215_K	2.417	1.00
15_K	18_R	2.394	1.00
336_S	339_I	2.377	1.00
356_C	405_V	2.367	1.00
266_T	270_T	2.353	1.00
138_I	208_F	2.330	1.00
331_K	337_P	2.316	1.00
139_V	212_G	2.281	1.00
261_N	264_Q	2.262	1.00
417_M	421_R	2.254	1.00
348_S	416_G	2.213	1.00
78_L	82_D	2.211	1.00
421_R	425_K	2.177	1.00
139_V	214_T	2.149	1.00
264_Q	268_D	2.052	1.00
79_E	82_D	2.050	1.00
352_G	412_A	2.038	1.00
140_V	145_A	2.017	1.00
29_T	358_I	2.004	1.00
359_G	363_S	1.967	1.00
397_P	400_L	1.954	1.00
262_V	266_T	1.927	1.00
144_F	148_L	1.915	1.00
36_V	363_S	1.915	1.00
25_I	29_T	1.912	1.00
263_E	266_T	1.897	1.00
126_L	131_V	1.875	1.00
130_R	211_V	1.869	1.00
134_S	137_E	1.869	1.00
88_V	257_D	1.860	1.00
86_S	257_D	1.831	1.00
323_R	326_E	1.828	1.00
341_R	421_R	1.794	1.00
230_S	233_F	1.762	1.00
86_S	268_D	1.761	1.00
138_I	229_I	1.745	1.00
232_Q	235_K	1.743	1.00
47_K	51_D	1.729	1.00
75_K	79_E	1.698	1.00
80_K	83_H	1.693	1.00
114_T	118_D	1.655	1.00
208_F	233_F	1.638	1.00
229_I	234_K	1.633	1.00
33_A	362_I	1.630	1.00
187_E	205_T	1.608	1.00
140_V	210_I	1.601	1.00
79_E	83_H	1.600	1.00
136_N	233_F	1.595	1.00
267_N	270_T	1.591	1.00
25_I	355_G	1.581	1.00
77_D	80_K	1.573	1.00
140_V	227_I	1.570	1.00
29_T	362_I	1.568	1.00
268_D	271_D	1.558	1.00
139_V	211_V	1.524	1.00
143_D	216_K	1.517	1.00
138_I	186_I	1.517	1.00
143_D	146_K	1.515	1.00
76_A	80_K	1.515	1.00
339_I	342_R	1.515	1.00
258_K	261_N	1.506	1.00
267_N	271_D	1.505	1.00
88_V	255_F	1.504	1.00
141_G	214_T	1.503	1.00
231_D	235_K	1.502	1.00
337_P	424_T	1.496	1.00
182_L	213_I	1.493	1.00
73_I	77_D	1.490	1.00
398_A	402_I	1.488	1.00
127_E	142_Y	1.482	1.00
140_V	144_F	1.473	1.00
130_R	137_E	1.468	1.00
12_R	15_K	1.459	1.00
52_M	55_S	1.452	1.00
263_E	267_N	1.442	1.00
420_A	424_T	1.440	1.00
252_I	256_A	1.436	1.00
43_F	397_P	1.425	1.00
13_N	347_E	1.425	1.00
365_G	369_L	1.419	1.00
256_A	265_L	1.415	1.00
278_S	281_T	1.393	1.00
399_S	403_I	1.391	1.00
229_I	233_F	1.371	1.00
338_S	342_R	1.365	1.00
355_G	359_G	1.350	1.00
132_A	137_E	1.347	1.00
132_A	211_V	1.337	1.00
415_S	419_P	1.332	1.00
28_T	355_G	1.331	1.00
14_M	21_V	1.327	1.00
51_D	54_M	1.307	1.00
326_E	330_M	1.307	1.00
352_G	356_C	1.305	1.00
76_A	79_E	1.301	1.00
29_T	33_A	1.300	1.00
102_G	105_T	1.293	1.00
40_S	367_S	1.290	1.00
324_T	431_A	1.290	1.00
327_I	340_I	1.283	1.00
365_G	368_Y	1.280	1.00
298_I	302_C	1.274	1.00
150_T	184_K	1.270	1.00
89_E	255_F	1.266	1.00
32_C	359_G	1.265	1.00
328_G	431_A	1.265	1.00
84_V	268_D	1.263	1.00
20_R	322_E	1.257	1.00
51_D	55_S	1.255	1.00
335_A	339_I	1.251	1.00
141_G	144_F	1.239	1.00
324_T	426_T	1.238	1.00
265_L	269_L	1.229	1.00
127_E	215_K	1.226	1.00
422_K	425_K	1.225	1.00
10_I	346_M	1.224	1.00
342_R	346_M	1.220	1.00
131_V	139_V	1.213	1.00
119_E	131_V	1.210	1.00
61_K	65_M	1.202	1.00
132_A	139_V	1.201	1.00
361_I	365_G	1.200	1.00
46_Q	50_T	1.197	1.00
330_M	335_A	1.193	1.00
47_K	395_Y	1.191	1.00
363_S	367_S	1.186	1.00
309_A	415_S	1.183	1.00
33_A	366_V	1.180	1.00
328_G	332_A	1.177	1.00
151_K	184_K	1.176	1.00
36_V	404_A	1.175	1.00
143_D	147_R	1.175	1.00
75_K	78_L	1.170	1.00
93_V	251_N	1.169	1.00
330_M	343_M	1.165	1.00
140_V	213_I	1.163	1.00
21_V	351_I	1.162	1.00
117_N	120_L	1.160	1.00
43_F	46_Q	1.150	1.00
357_V	361_I	1.149	1.00
33_A	363_S	1.143	1.00
182_L	211_V	1.141	1.00
189_S	205_T	1.138	1.00
233_F	236_D	1.137	1.00
402_I	406_V	1.137	1.00
31_A	301_G	1.135	1.00
142_Y	216_K	1.134	1.00
295_I	299_F	1.117	1.00
17_N	322_E	1.115	1.00
19_L	22_F	1.111	1.00
133_K	136_N	1.110	1.00
43_F	400_L	1.101	1.00
190_V	204_K	1.100	1.00
284_E	288_T	1.099	1.00
136_N	206_Y	1.098	1.00
86_S	265_L	1.090	1.00
316_M	348_S	1.089	1.00
33_A	359_G	1.082	1.00
395_Y	398_A	1.078	1.00
150_T	210_I	1.074	1.00
421_R	424_T	1.059	1.00
11_R	15_K	1.058	1.00
47_K	50_T	1.045	1.00
399_S	402_I	1.044	1.00
126_L	212_G	1.043	1.00
369_L	373_A	1.043	1.00
358_I	361_I	1.040	1.00
356_C	408_C	1.038	1.00
370_V	374_V	1.036	1.00
128_K	182_L	1.034	1.00
192_K	204_K	1.032	1.00
368_Y	372_L	1.032	1.00
84_V	87_V	1.027	1.00
46_Q	294_K	1.026	1.00
262_V	265_L	1.013	1.00
60_T	64_V	1.010	1.00
22_F	26_L	1.008	1.00
287_N	291_M	1.005	1.00
25_I	354_L	1.005	1.00
77_D	81_Y	0.999	1.00
84_V	265_L	0.999	1.00
341_R	417_M	0.996	1.00
422_K	426_T	0.987	1.00
133_K	137_E	0.983	1.00
264_Q	267_N	0.980	1.00
304_A	311_G	0.977	1.00
280_T	284_E	0.970	1.00
50_T	54_M	0.965	1.00
89_E	121_K	0.964	1.00
426_T	430_T	0.964	1.00
43_F	47_K	0.958	1.00
135_E	232_Q	0.957	1.00
281_T	284_E	0.955	1.00
53_T	56_Q	0.950	1.00
349_A	413_V	0.946	1.00
234_K	237_F	0.945	1.00
250_T	253_G	0.944	1.00
313_F	317_T	0.943	1.00
288_T	291_M	0.940	1.00
290_F	294_K	0.940	1.00
256_A	262_V	0.938	1.00
128_K	213_I	0.932	1.00
408_C	412_A	0.931	1.00
291_M	295_I	0.929	1.00
309_A	411_V	0.925	1.00
352_G	408_C	0.922	1.00
348_S	352_G	0.922	1.00
370_V	373_A	0.921	1.00
335_A	340_I	0.915	1.00
360_I	401_V	0.913	1.00
231_D	234_K	0.905	1.00
369_L	372_L	0.905	1.00
323_R	344_F	0.905	1.00
89_E	120_L	0.902	1.00
418_N	421_R	0.902	1.00
266_T	278_S	0.895	1.00
25_I	358_I	0.893	1.00
420_A	423_A	0.893	1.00
337_P	425_K	0.892	1.00
40_S	44_G	0.892	1.00
372_L	375_P	0.889	1.00
17_N	20_R	0.886	1.00
29_T	32_C	0.879	1.00
74_K	78_L	0.879	1.00
142_Y	145_A	0.878	1.00
29_T	355_G	0.878	1.00
32_C	408_C	0.877	1.00
101_L	104_R	0.876	1.00
73_I	76_A	0.874	1.00
337_P	341_R	0.873	1.00
403_I	406_V	0.871	1.00
141_G	216_K	0.864	1.00
426_T	431_A	0.852	1.00
78_L	92_Q	0.852	1.00
48_T	52_M	0.851	1.00
257_D	261_N	0.851	1.00
331_K	428_V	0.849	1.00
91_T	115_N	0.848	1.00
428_V	431_A	0.846	1.00
27_A	311_G	0.843	1.00
35_L	39_S	0.842	1.00
396_I	401_V	0.838	1.00
82_D	90_R	0.836	1.00
140_V	150_T	0.833	1.00
61_K	66_G	0.830	1.00
404_A	408_C	0.830	1.00
368_Y	371_N	0.828	1.00
341_R	424_T	0.827	1.00
345_L	413_V	0.825	1.00
321_T	324_T	0.822	1.00
78_L	81_Y	0.820	1.00
61_K	64_V	0.819	1.00
115_N	118_D	0.818	1.00
403_I	407_I	0.817	1.00
324_T	328_G	0.816	1.00
28_T	32_C	0.816	1.00
341_R	420_A	0.813	1.00
27_A	31_A	0.810	1.00
120_L	131_V	0.808	1.00
111_L	229_I	0.808	1.00
109_S	144_F	0.807	1.00
237_F	240_F	0.807	1.00
60_T	63_S	0.805	1.00
356_C	412_A	0.802	1.00
361_I	364_Y	0.801	1.00
234_K	238_S	0.801	1.00
13_N	326_E	0.801	1.00
279_V	282_E	0.799	1.00
53_T	57_Q	0.798	1.00
87_V	90_R	0.797	1.00
313_F	415_S	0.797	1.00
24_T	27_A	0.793	1.00
320_V	327_I	0.790	1.00
405_V	409_G	0.788	1.00
360_I	405_V	0.787	1.00
331_K	340_I	0.787	1.00
250_T	254_V	0.786	1.00
149_L	184_K	0.785	1.00
367_S	371_N	0.780	1.00
24_T	315_T	0.779	1.00
214_T	228_F	0.778	1.00
256_A	259_F	0.776	1.00
265_L	268_D	0.776	1.00
111_L	227_I	0.773	1.00
406_V	410_G	0.772	1.00
63_S	66_G	0.771	1.00
400_L	403_I	0.771	1.00
401_V	405_V	0.769	1.00
285_G	288_T	0.769	1.00
113_F	234_K	0.769	1.00
146_K	151_K	0.765	1.00
410_G	414_I	0.764	1.00
92_Q	115_N	0.762	1.00
354_L	357_V	0.756	1.00
99_A	102_G	0.754	1.00
23_M	27_A	0.750	1.00
18_R	22_F	0.750	1.00
188_L	208_F	0.750	1.00
98_K	101_L	0.749	1.00
124_M	214_T	0.746	1.00
50_T	53_T	0.743	1.00
9_F	13_N	0.740	1.00
241_L	247_N	0.738	1.00
319_A	347_E	0.738	1.00
126_L	214_T	0.737	1.00
395_Y	399_S	0.737	1.00
145_A	151_K	0.736	1.00
328_G	428_V	0.736	1.00
93_V	96_P	0.732	1.00
151_K	182_L	0.731	1.00
349_A	412_A	0.729	1.00
260_E	265_L	0.728	1.00
429_L	433_R	0.728	1.00
37_V	366_V	0.725	1.00
260_E	264_Q	0.724	1.00
109_S	227_I	0.723	1.00
94_Y	234_K	0.722	1.00
418_N	422_K	0.721	1.00
364_Y	396_I	0.721	1.00
348_S	419_P	0.719	1.00
283_L	287_N	0.718	1.00
346_M	349_A	0.717	1.00
54_M	57_Q	0.717	1.00
362_I	365_G	0.716	1.00
9_F	343_M	0.714	1.00
182_L	212_G	0.714	1.00
88_V	91_T	0.714	1.00
93_V	253_G	0.710	1.00
356_C	360_I	0.709	1.00
78_L	90_R	0.709	1.00
314_N	318_M	0.708	1.00
356_C	409_G	0.708	1.00
301_G	305_V	0.708	1.00
140_V	186_I	0.708	1.00
48_T	51_D	0.707	1.00
429_L	432_L	0.706	1.00
325_Q	329_I	0.704	1.00
316_M	319_A	0.703	1.00
319_A	323_R	0.702	1.00
249_E	252_I	0.702	1.00
311_G	314_N	0.702	1.00
348_S	420_A	0.700	1.00
36_V	40_S	0.698	1.00
138_I	210_I	0.697	1.00
9_F	330_M	0.695	1.00
27_A	314_N	0.694	1.00
13_N	323_R	0.693	1.00
141_G	225_S	0.693	1.00
135_E	230_S	0.692	1.00
346_M	350_Y	0.692	1.00
407_I	410_G	0.692	1.00
206_Y	236_D	0.692	1.00
226_N	230_S	0.691	1.00
94_Y	97_N	0.689	1.00
191_S	204_K	0.687	1.00
416_G	420_A	0.686	1.00
302_C	306_I	0.685	1.00
89_E	92_Q	0.683	1.00
183_N	209_K	0.680	1.00
88_V	92_Q	0.680	1.00
364_Y	368_Y	0.679	1.00
99_A	106_N	0.678	1.00
329_I	332_A	0.676	1.00
89_E	117_N	0.675	1.00
226_N	229_I	0.671	1.00
257_D	260_E	0.669	1.00
122_A	125_E	0.668	1.00
92_Q	249_E	0.665	1.00
145_A	182_L	0.662	1.00
113_F	116_M	0.659	1.00
37_V	363_S	0.659	1.00
308_S	311_G	0.658	1.00
82_D	89_E	0.658	1.00
19_L	23_M	0.657	1.00
126_L	130_R	0.657	1.00
125_E	129_G	0.656	1.00
141_G	226_N	0.656	1.00
290_F	293_F	0.656	1.00
252_I	255_F	0.654	1.00
348_S	412_A	0.652	1.00
39_S	43_F	0.651	1.00
90_R	93_V	0.650	1.00
42_G	294_K	0.650	1.00
304_A	308_S	0.649	1.00
87_V	254_V	0.647	1.00
288_T	292_V	0.645	1.00
419_P	423_A	0.644	1.00
128_K	145_A	0.644	1.00
253_G	256_A	0.642	1.00
115_N	231_D	0.642	1.00
53_T	58_I	0.641	1.00
315_T	319_A	0.641	1.00
10_I	343_M	0.640	1.00
398_A	401_V	0.639	1.00
345_L	417_M	0.638	1.00
411_V	415_S	0.636	1.00
81_Y	269_L	0.635	1.00
52_M	56_Q	0.634	1.00
117_N	121_K	0.633	1.00
129_G	132_A	0.629	1.00
353_I	409_G	0.628	1.00
277_T	282_E	0.626	1.00
92_Q	95_E	0.625	1.00
392_T	395_Y	0.625	1.00
400_L	404_A	0.624	1.00
126_L	139_V	0.623	1.00
126_L	132_A	0.622	1.00
251_N	254_V	0.621	1.00
81_Y	84_V	0.620	1.00
142_Y	213_I	0.619	1.00
31_A	311_G	0.619	1.00
208_F	229_I	0.618	1.00
110_N	113_F	0.618	1.00
101_L	106_N	0.617	1.00
352_G	416_G	0.615	1.00
407_I	411_V	0.613	1.00
294_K	298_I	0.611	1.00
127_E	214_T	0.611	1.00
419_P	424_T	0.610	1.00
65_M	277_T	0.609	1.00
28_T	312_I	0.607	1.00
347_E	350_Y	0.606	1.00
135_E	233_F	0.604	1.00
126_L	215_K	0.604	1.00
396_I	400_L	0.603	1.00
78_L	252_I	0.603	1.00
320_V	344_F	0.603	1.00
107_E	147_R	0.603	1.00
364_Y	401_V	0.602	1.00
45_I	48_T	0.601	1.00
36_V	359_G	0.600	1.00
31_A	34_F	0.600	1.00
186_I	208_F	0.596	1.00
277_T	281_T	0.595	1.00
40_S	363_S	0.593	1.00
49_I	53_T	0.592	1.00
275_Y	278_S	0.592	1.00
249_E	253_G	0.591	1.00
235_K	238_S	0.591	1.00
270_T	276_V	0.591	1.00
33_A	37_V	0.590	1.00
91_T	94_Y	0.589	1.00
136_N	209_K	0.589	1.00
54_M	58_I	0.587	1.00
145_A	148_L	0.587	1.00
329_I	333_I	0.587	1.00
273_G	276_V	0.586	1.00
343_M	346_M	0.586	1.00
251_N	255_F	0.585	1.00
256_A	261_N	0.585	1.00
118_D	121_K	0.585	1.00
11_R	350_Y	0.585	1.00
292_V	296_G	0.583	1.00
326_E	329_I	0.583	1.00
390_N	393_F	0.580	1.00
282_E	285_G	0.579	1.00
90_R	254_V	0.579	1.00
80_K	84_V	0.579	1.00
109_S	112_I	0.578	1.00
344_F	348_S	0.578	1.00
321_T	422_K	0.577	1.00
320_V	423_A	0.576	1.00
139_V	228_F	0.574	1.00
67_K	70_D	0.573	1.00
129_G	212_G	0.573	1.00
341_R	345_L	0.571	1.00
43_F	399_S	0.571	1.00
121_K	255_F	0.569	1.00
307_I	311_G	0.568	1.00
55_S	58_I	0.568	1.00
98_K	102_G	0.568	1.00
102_G	106_N	0.567	1.00
233_F	237_F	0.564	1.00
284_E	287_N	0.563	1.00
324_T	422_K	0.562	1.00
18_R	21_V	0.561	1.00
345_L	349_A	0.559	1.00
91_T	121_K	0.559	1.00
274_Y	278_S	0.558	1.00
296_G	300_V	0.553	1.00
113_F	231_D	0.551	1.00
112_I	228_F	0.551	1.00
88_V	256_A	0.551	1.00
183_N	186_I	0.547	1.00
371_N	374_V	0.546	1.00
62_V	266_T	0.546	1.00
140_V	149_L	0.546	1.00
127_E	213_I	0.545	1.00
326_E	347_E	0.544	1.00
262_V	278_S	0.542	1.00
85_R	88_V	0.537	1.00
100_T	109_S	0.535	1.00
62_V	254_V	0.535	1.00
95_E	110_N	0.533	1.00
316_M	416_G	0.533	1.00
344_F	420_A	0.529	1.00
326_E	343_M	0.529	1.00
42_G	297_L	0.528	1.00
100_T	103_N	0.528	1.00
256_A	260_E	0.526	1.00
111_L	114_T	0.525	1.00
184_K	210_I	0.524	1.00
86_S	261_N	0.524	1.00
236_D	239_E	0.523	1.00
27_A	318_M	0.523	1.00
24_T	28_T	0.522	1.00
49_I	52_M	0.521	1.00
287_N	290_F	0.519	1.00
145_A	210_I	0.519	1.00
218_S	224_D	0.516	1.00
332_A	428_V	0.515	1.00
228_F	231_D	0.514	1.00
368_Y	393_F	0.514	1.00
46_Q	49_I	0.513	1.00
266_T	269_L	0.513	1.00
338_S	341_R	0.511	1.00
145_A	150_T	0.510	1.00
61_K	67_K	0.510	1.00
98_K	111_L	0.510	1.00
235_K	239_E	0.510	1.00
309_A	313_F	0.509	1.00
428_V	433_R	0.506	1.00
87_V	265_L	0.504	1.00
367_S	393_F	0.503	1.00
29_T	359_G	0.503	1.00
360_I	364_Y	0.503	1.00
111_L	115_N	0.503	1.00
13_N	20_R	0.503	1.00
112_I	226_N	0.502	1.00
208_F	237_F	0.501	1.00
344_F	347_E	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
3ftjA	1	0.4381	99.3	0.752	Contact Map
3is6A	2	0.4977	98.8	0.798	Contact Map
4il3A	1	0.4358	13.1	0.951	Contact Map
2f95B	2	0.1216	10.9	0.953	Contact Map
2kogA	1	0.094	9.1	0.955	Contact Map
4pl0A	2	0.2225	8.7	0.955	Contact Map
2l66A	2	0.1216	7.7	0.956	Contact Map
4gycB	2	0.1399	5.9	0.958	Contact Map
3zdqA	2	0.2225	5.7	0.958	Contact Map
1yfbA	2	0.1193	4.9	0.96	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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