YVRB - BACSU - GREMLIN Contacts

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YVRB - Uncharacterized ABC transporter permease protein YvrB

UniProt:	O34451	Sequences: MRKAFTRIRLRNNRYAAYIIGFSFLAVSIILGISCGSLHIPIPAVFRVFWHQGFGGSIGSDDPMYTNIMMNIRLPRVVLAALVGAALSIAGAAFQGLLKNPLADPYTLGVSSGASVGAVVTLFLGLHLPVIGGFTLPVLSVAAALATMAAVLFFSRLVHASMSVSTLILTGVITNSFLGAFISLIIALTGDNLLPIVHWLLGSVSMRGWSYVILFLPFFLLGTILLIINGRELNVMTYGEDKAKLLGVSVQQRKMMILIAGSLLTGSAVAVSGTIGFVGLVIPHITRLLWGTDHRHLLPLSALLGAGFLVLADLLSRTIIEPIELPIGIITSLAGAPVFALILIRQHRGGRSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	353 (320)
Sequences:	13908 (9941)
Seq/√Len:	555.7

ECOLI - FEPG FEPD FECC BTUC FECD FHUB
BACSU - YVRB FHUB YFME FHUG YFHA YFIZ FEUB YFMD FEUC YCLN YCLO
HALSA - Q9HMG0 Q9HMG7 BTUCA
SULSO - Q97ZU1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
234_N	293_D	5.059	1.00
85_A	302_A	3.803	1.00
121_T	139_L	3.657	1.00
93_A	226_L	3.633	1.00
28_S	311_L	3.628	1.00
29_I	77_V	3.426	1.00
249_S	252_Q	3.285	1.00
86_A	219_F	3.261	1.00
81_A	306_A	3.179	1.00
93_A	257_I	3.119	1.00
80_A	204_V	2.985	1.00
286_T	304_L	2.907	1.00
79_L	207_R	2.747	1.00
86_A	264_L	2.670	1.00
86_A	268_A	2.614	1.00
44_A	65_Y	2.552	1.00
29_I	81_A	2.440	1.00
89_I	302_A	2.422	1.00
240_E	254_K	2.373	1.00
116_V	181_F	2.371	1.00
24_F	307_G	2.361	1.00
44_A	47_R	2.346	1.00
25_L	307_G	2.338	1.00
89_I	223_T	2.276	1.00
83_V	268_A	2.256	1.00
116_V	178_L	2.234	1.00
34_S	42_I	2.176	1.00
92_A	301_S	2.162	1.00
290_W	300_L	2.144	1.00
234_N	294_H	2.121	1.00
83_V	272_S	2.109	1.00
76_R	313_D	2.082	1.00
32_G	77_V	2.043	1.00
62_D	65_Y	2.028	1.00
81_A	310_V	2.014	1.00
25_L	81_A	2.009	1.00
82_L	216_L	1.951	1.00
218_F	267_S	1.935	1.00
96_G	294_H	1.923	1.00
28_S	307_G	1.871	1.00
232_E	253_R	1.854	1.00
41_P	44_A	1.839	1.00
120_V	124_L	1.813	1.00
94_F	261_G	1.796	1.00
119_V	182_I	1.789	1.00
207_R	211_Y	1.771	1.00
235_V	248_V	1.757	1.00
18_Y	300_L	1.717	1.00
144_A	266_G	1.691	1.00
229_N	232_E	1.687	1.00
225_L	260_A	1.630	1.00
315_L	319_I	1.608	1.00
25_L	303_L	1.608	1.00
43_P	47_R	1.606	1.00
278_V	309_L	1.599	1.00
316_S	327_I	1.573	1.00
78_V	212_V	1.564	1.00
118_A	140_S	1.556	1.00
63_P	66_T	1.540	1.00
222_G	264_L	1.532	1.00
252_Q	256_M	1.531	1.00
117_G	139_L	1.519	1.00
229_N	256_M	1.508	1.00
46_F	50_W	1.504	1.00
28_S	310_V	1.497	1.00
31_L	34_S	1.497	1.00
148_M	262_S	1.496	1.00
222_G	263_L	1.487	1.00
66_T	70_M	1.462	1.00
286_T	297_L	1.462	1.00
315_L	330_I	1.452	1.00
21_G	303_L	1.446	1.00
92_A	297_L	1.438	1.00
48_V	70_M	1.436	1.00
21_G	300_L	1.429	1.00
90_A	264_L	1.428	1.00
17_A	300_L	1.428	1.00
115_S	182_I	1.418	1.00
213_I	217_P	1.415	1.00
213_I	216_L	1.386	1.00
204_V	309_L	1.380	1.00
208_G	211_Y	1.376	1.00
31_L	35_C	1.371	1.00
229_N	253_R	1.367	1.00
79_L	271_V	1.361	1.00
296_H	299_P	1.329	1.00
222_G	260_A	1.323	1.00
32_G	314_L	1.316	1.00
111_S	265_T	1.312	1.00
282_I	308_F	1.306	1.00
317_R	324_E	1.300	1.00
117_G	143_A	1.300	1.00
177_F	336_A	1.293	1.00
88_S	282_I	1.286	1.00
286_T	300_L	1.266	1.00
217_P	221_L	1.256	1.00
294_H	297_L	1.241	1.00
82_L	212_V	1.230	1.00
147_T	178_L	1.227	1.00
225_L	229_N	1.226	1.00
229_N	257_I	1.225	1.00
21_G	304_L	1.217	1.00
92_A	294_H	1.207	1.00
151_V	174_T	1.193	1.00
115_S	200_L	1.191	1.00
141_V	263_L	1.190	1.00
113_G	143_A	1.182	1.00
97_L	257_I	1.177	1.00
18_Y	296_H	1.174	1.00
253_R	256_M	1.162	1.00
282_I	304_L	1.161	1.00
244_K	251_Q	1.155	1.00
252_Q	255_M	1.147	1.00
119_V	196_I	1.143	1.00
275_I	309_L	1.141	1.00
116_V	120_V	1.137	1.00
38_L	68_I	1.132	1.00
239_G	243_A	1.122	1.00
149_A	153_F	1.121	1.00
25_L	306_A	1.118	1.00
313_D	317_R	1.114	1.00
48_V	66_T	1.113	1.00
82_L	215_F	1.108	1.00
242_K	245_L	1.105	1.00
67_N	71_N	1.101	1.00
251_Q	254_K	1.097	1.00
70_M	74_L	1.092	1.00
39_H	42_I	1.087	1.00
92_A	298_L	1.082	1.00
123_F	185_I	1.079	1.00
21_G	307_G	1.075	1.00
138_V	142_A	1.074	1.00
48_V	61_D	1.072	1.00
80_A	309_L	1.071	1.00
33_I	77_V	1.071	1.00
79_L	212_V	1.071	1.00
215_F	271_V	1.069	1.00
272_S	275_I	1.068	1.00
85_A	88_S	1.067	1.00
61_D	66_T	1.062	1.00
51_H	61_D	1.057	1.00
29_I	310_V	1.051	1.00
315_L	318_T	1.051	1.00
235_V	246_L	1.050	1.00
78_V	209_W	1.046	1.00
332_S	337_P	1.038	1.00
146_A	150_A	1.036	1.00
28_S	314_L	1.034	1.00
80_A	310_V	1.034	1.00
226_L	260_A	1.030	1.00
64_M	67_N	1.029	1.00
48_V	69_M	1.027	1.00
307_G	311_L	1.026	1.00
222_G	267_S	1.026	1.00
225_L	256_M	1.022	1.00
215_F	219_F	1.014	1.00
299_P	302_A	1.013	1.00
294_H	299_P	1.012	1.00
77_V	314_L	1.011	1.00
45_V	69_M	1.004	1.00
85_A	306_A	0.999	1.00
139_L	143_A	0.987	1.00
16_A	19_I	0.981	1.00
132_G	135_T	0.981	1.00
35_C	318_T	0.979	1.00
156_R	251_Q	0.974	1.00
282_I	286_T	0.969	1.00
113_G	147_T	0.967	1.00
120_V	185_I	0.966	1.00
184_L	188_L	0.961	1.00
15_Y	18_Y	0.956	1.00
290_W	296_H	0.953	1.00
224_I	228_I	0.953	1.00
221_L	224_I	0.951	1.00
30_I	34_S	0.945	1.00
241_D	244_K	0.942	1.00
112_S	178_L	0.940	1.00
175_N	179_G	0.939	1.00
297_L	301_S	0.932	1.00
111_S	274_T	0.928	1.00
251_Q	255_M	0.927	1.00
34_S	45_V	0.914	1.00
152_L	251_Q	0.912	1.00
209_W	212_V	0.912	1.00
296_H	300_L	0.911	1.00
316_S	330_I	0.911	1.00
214_L	217_P	0.904	1.00
116_V	182_I	0.902	1.00
23_S	27_V	0.900	1.00
22_F	26_A	0.898	1.00
156_R	159_H	0.893	1.00
316_S	326_P	0.893	1.00
311_L	315_L	0.892	1.00
253_R	257_I	0.891	1.00
91_G	283_P	0.888	1.00
248_V	253_R	0.887	1.00
118_A	136_L	0.886	1.00
268_A	272_S	0.883	1.00
60_S	63_P	0.875	1.00
116_V	185_I	0.874	1.00
47_R	50_W	0.865	1.00
47_R	51_H	0.863	1.00
30_I	42_I	0.862	1.00
48_V	65_Y	0.860	1.00
86_A	90_A	0.860	1.00
338_V	341_L	0.858	1.00
320_I	323_I	0.857	1.00
233_L	257_I	0.857	1.00
15_Y	19_I	0.856	1.00
16_A	20_I	0.854	1.00
112_S	115_S	0.854	1.00
17_A	20_I	0.852	1.00
76_R	317_R	0.851	1.00
106_Y	111_S	0.850	1.00
226_L	257_I	0.849	1.00
217_P	220_L	0.849	1.00
156_R	161_S	0.848	1.00
66_T	71_N	0.846	1.00
234_N	295_R	0.846	1.00
82_L	219_F	0.846	1.00
85_A	223_T	0.841	1.00
122_L	136_L	0.837	1.00
36_G	73_R	0.835	1.00
289_L	304_L	0.833	1.00
293_D	296_H	0.825	1.00
230_G	295_R	0.824	1.00
144_A	262_S	0.823	1.00
110_V	144_A	0.817	1.00
90_A	261_G	0.816	1.00
319_I	322_P	0.816	1.00
220_L	224_I	0.813	1.00
17_A	21_G	0.805	1.00
196_I	200_L	0.802	1.00
26_A	30_I	0.801	1.00
76_R	324_E	0.800	1.00
225_L	228_I	0.800	1.00
40_I	69_M	0.799	1.00
240_E	244_K	0.799	1.00
218_F	222_G	0.796	1.00
229_N	260_A	0.795	1.00
318_T	321_E	0.794	1.00
77_V	310_V	0.794	1.00
114_A	144_A	0.793	1.00
337_P	341_L	0.792	1.00
333_L	337_P	0.791	1.00
142_A	146_A	0.788	1.00
309_L	331_T	0.788	1.00
61_D	65_Y	0.784	1.00
145_L	266_G	0.784	1.00
98_L	168_I	0.783	1.00
51_H	60_S	0.779	1.00
85_A	219_F	0.777	1.00
243_A	250_V	0.777	1.00
40_I	65_Y	0.771	1.00
26_A	29_I	0.769	1.00
120_V	125_G	0.765	1.00
22_F	303_L	0.763	1.00
240_E	250_V	0.763	1.00
25_L	29_I	0.762	1.00
287_R	297_L	0.761	1.00
45_V	48_V	0.759	1.00
131_I	135_T	0.759	1.00
104_D	107_T	0.758	1.00
121_T	136_L	0.755	1.00
88_S	302_A	0.751	1.00
194_L	197_V	0.750	1.00
152_L	255_M	0.749	1.00
88_S	92_A	0.749	1.00
189_T	192_N	0.747	1.00
119_V	186_I	0.744	1.00
74_L	209_W	0.743	1.00
27_V	30_I	0.739	1.00
141_V	145_L	0.739	1.00
258_L	262_S	0.737	1.00
147_T	151_V	0.737	1.00
156_R	162_M	0.736	1.00
295_R	299_P	0.736	1.00
25_L	310_V	0.732	1.00
148_M	258_L	0.732	1.00
89_I	226_L	0.729	1.00
286_T	290_W	0.729	1.00
286_T	289_L	0.728	1.00
87_L	278_V	0.726	1.00
38_L	41_P	0.725	1.00
278_V	331_T	0.725	1.00
320_I	325_L	0.723	1.00
94_F	108_L	0.722	1.00
115_S	274_T	0.722	1.00
151_V	155_S	0.719	1.00
34_S	39_H	0.718	1.00
250_V	254_K	0.717	1.00
78_V	82_L	0.716	1.00
255_M	259_I	0.715	1.00
308_F	312_A	0.715	1.00
38_L	42_I	0.713	1.00
32_G	317_R	0.710	1.00
234_N	299_P	0.709	1.00
60_S	66_T	0.709	1.00
285_I	304_L	0.709	1.00
17_A	289_L	0.705	1.00
96_G	237_T	0.705	1.00
219_F	268_A	0.703	1.00
303_L	307_G	0.703	1.00
313_D	324_E	0.699	1.00
211_Y	271_V	0.698	1.00
267_S	270_A	0.695	1.00
79_L	215_F	0.687	1.00
215_F	267_S	0.686	1.00
51_H	66_T	0.686	1.00
135_T	138_V	0.685	1.00
267_S	271_V	0.684	1.00
110_V	148_M	0.674	1.00
40_I	48_V	0.673	1.00
27_V	31_L	0.672	1.00
288_L	342_I	0.672	1.00
104_D	279_G	0.670	1.00
197_V	200_L	0.669	1.00
227_I	230_G	0.667	1.00
21_G	25_L	0.665	1.00
153_F	156_R	0.664	1.00
33_I	69_M	0.663	1.00
275_I	327_I	0.663	1.00
83_V	204_V	0.660	1.00
89_I	298_L	0.659	1.00
210_S	213_I	0.658	1.00
341_L	345_R	0.657	1.00
120_V	181_F	0.657	1.00
244_K	250_V	0.656	1.00
67_N	72_I	0.653	1.00
90_A	265_T	0.653	1.00
312_A	330_I	0.652	1.00
216_L	220_L	0.651	1.00
191_D	194_L	0.650	1.00
189_T	193_L	0.646	1.00
306_A	310_V	0.644	1.00
155_S	170_T	0.644	1.00
63_P	67_N	0.639	1.00
228_I	232_E	0.637	1.00
122_L	195_P	0.637	1.00
261_G	266_G	0.636	1.00
113_G	178_L	0.636	1.00
154_F	170_T	0.633	1.00
222_G	226_L	0.630	1.00
30_I	46_F	0.629	1.00
94_F	103_A	0.629	1.00
232_E	248_V	0.628	1.00
285_I	288_L	0.627	1.00
74_L	78_V	0.627	1.00
33_I	74_L	0.626	1.00
234_N	237_T	0.626	1.00
123_F	189_T	0.625	1.00
67_N	70_M	0.624	1.00
94_F	110_V	0.619	1.00
42_I	46_F	0.618	1.00
98_L	101_P	0.618	1.00
218_F	263_L	0.618	1.00
302_A	306_A	0.617	1.00
283_P	301_S	0.617	1.00
93_A	260_A	0.617	1.00
280_L	342_I	0.617	1.00
85_A	89_I	0.616	1.00
191_D	195_P	0.615	1.00
145_L	262_S	0.612	1.00
43_P	46_F	0.609	1.00
117_G	121_T	0.608	1.00
308_F	334_A	0.608	1.00
156_R	160_A	0.607	1.00
311_L	314_L	0.607	1.00
80_A	327_I	0.606	1.00
165_S	168_I	0.606	1.00
42_I	45_V	0.606	1.00
29_I	33_I	0.603	1.00
111_S	114_A	0.601	1.00
25_L	77_V	0.599	1.00
186_I	197_V	0.599	1.00
62_D	66_T	0.598	1.00
183_S	199_W	0.597	1.00
122_L	196_I	0.596	1.00
45_V	49_F	0.594	1.00
35_C	39_H	0.593	1.00
223_T	227_I	0.592	1.00
41_P	65_Y	0.591	1.00
215_F	218_F	0.590	1.00
236_M	250_V	0.588	1.00
114_A	140_S	0.587	1.00
281_V	339_F	0.587	1.00
316_S	324_E	0.586	1.00
310_V	314_L	0.586	1.00
170_T	173_I	0.584	1.00
143_A	147_T	0.584	1.00
204_V	327_I	0.584	1.00
88_S	305_G	0.583	1.00
136_L	139_L	0.582	1.00
127_H	131_I	0.581	1.00
265_T	269_V	0.580	1.00
266_G	270_A	0.580	1.00
280_L	283_P	0.580	1.00
221_L	225_L	0.578	0.99
209_W	213_I	0.576	0.99
233_L	294_H	0.575	0.99
103_A	110_V	0.572	0.99
44_A	51_H	0.572	0.99
285_I	308_F	0.570	0.99
192_N	195_P	0.567	0.99
285_I	338_V	0.566	0.99
134_F	138_V	0.566	0.99
309_L	327_I	0.565	0.99
286_T	301_S	0.564	0.99
69_M	74_L	0.564	0.99
34_S	46_F	0.564	0.99
344_I	347_H	0.564	0.99
146_A	149_A	0.563	0.99
20_I	24_F	0.561	0.99
44_A	61_D	0.561	0.99
187_A	329_I	0.561	0.99
183_S	187_A	0.560	0.99
193_L	196_I	0.560	0.99
314_L	318_T	0.559	0.99
186_I	200_L	0.558	0.99
232_E	235_V	0.557	0.99
219_F	224_I	0.554	0.99
47_R	61_D	0.554	0.99
281_V	338_V	0.550	0.99
256_M	260_A	0.549	0.99
278_V	308_F	0.548	0.99
97_L	261_G	0.547	0.99
104_D	274_T	0.547	0.99
110_V	203_S	0.546	0.99
92_A	286_T	0.546	0.99
104_D	331_T	0.545	0.99
37_S	322_P	0.545	0.99
275_I	331_T	0.543	0.99
214_L	267_S	0.541	0.99
179_G	183_S	0.541	0.99
29_I	78_V	0.538	0.99
228_I	231_R	0.536	0.99
262_S	266_G	0.536	0.99
204_V	272_S	0.536	0.99
124_L	127_H	0.534	0.99
112_S	175_N	0.534	0.99
152_L	156_R	0.533	0.99
313_D	322_P	0.533	0.99
79_L	83_V	0.532	0.99
110_V	151_V	0.531	0.99
179_G	200_L	0.530	0.99
212_V	216_L	0.529	0.99
18_Y	22_F	0.529	0.99
163_S	166_T	0.529	0.99
112_S	179_G	0.528	0.99
19_I	23_S	0.528	0.99
17_A	290_W	0.527	0.99
316_S	319_I	0.527	0.99
118_A	139_L	0.524	0.99
249_S	256_M	0.524	0.99
231_R	234_N	0.523	0.99
291_G	299_P	0.521	0.99
35_C	314_L	0.520	0.99
31_L	314_L	0.519	0.99
78_V	216_L	0.519	0.99
148_M	152_L	0.517	0.99
257_I	261_G	0.516	0.99
89_I	219_F	0.516	0.99
45_V	50_W	0.513	0.99
214_L	218_F	0.513	0.99
121_T	125_G	0.513	0.99
184_L	329_I	0.512	0.99
281_V	285_I	0.510	0.99
170_T	174_T	0.509	0.99
155_S	167_L	0.508	0.99
194_L	200_L	0.507	0.99
180_A	281_V	0.507	0.99
28_S	31_L	0.507	0.99
113_G	174_T	0.506	0.99
142_A	145_L	0.505	0.99
98_L	166_T	0.505	0.99
186_I	193_L	0.504	0.99
276_G	281_V	0.504	0.99
20_I	23_S	0.503	0.99
23_S	26_A	0.501	0.99
150_A	153_F	0.500	0.99

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
4g1uA	2	0.8385	100	0.23	Contact Map
2nq2A	2	0.8697	100	0.232	Contact Map
2qi9A	2	0.9065	100	0.244	Contact Map
2m8rA	1	0.1076	50	0.957	Contact Map
3rlbA	1	0.4788	16.4	0.967	Contact Map
2m20A	2	0.0822	16.4	0.967	Contact Map
4z7fA	2	0.4646	14	0.968	Contact Map
4huqS	1	0.4391	13	0.968	Contact Map
4tkrA	2	0.4873	9.1	0.97	Contact Map
3wajA	1	0.7564	9.1	0.97	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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