YBHR - ECOLI - GREMLIN Contacts

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YBHR - Inner membrane transport permease YbhR

UniProt:	P0AFP9	Sequences: MFHRLWTLIRKELQSLLREPQTRAILILPVLIQVILFPFAATLEVTNATIAIYDEDNGEHSVELTQRFARASAFTHVLLLKSPQEIRPTIDTQKALLLVRFPADFSRKLDTFQTAPLQLILDGRNSNSAQIAANYLQQIVKNYQQELLEGKPKPNNSELVVRNWYNPNLDYKWFVVPSLIAMITTIGVMIVTSLSVAREREQGTLDQLLVSPLTTWQIFIGKAVPALIVATFQATIVLAIGIWAYQIPFAGSLALFYFTMVIYGLSLVGFGLLISSLCSTQQQAFIGVFVFMMPAILLSGYVSPVENMPVWLQNLTWINPIRHFTDITKQIYLKDASLDIVWNSLWPLLVITATTGSAAYAMFRRKVM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13674
Length:	368 (348)
Sequences:	11105 (9157)
Seq/√Len:	490.9

ECOLI - YBHR YBHS YHHJ
BACSU - YFIM YFIN NATB YHAP YHGE
SULSO - Q97W41 Q7LY08 Q97WP5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_A	95_A	5.345	1.00
86_I	98_L	4.715	1.00
259_T	327_I	4.711	1.00
82_S	85_E	4.183	1.00
104_D	108_K	3.807	1.00
108_K	113_Q	3.729	1.00
89_T	95_A	3.668	1.00
8_L	221_G	3.576	1.00
10_R	14_Q	3.289	1.00
88_P	92_T	3.198	1.00
9_I	228_I	3.150	1.00
83_P	87_R	2.933	1.00
9_I	224_V	2.727	1.00
87_R	91_D	2.642	1.00
5_L	224_V	2.503	1.00
12_E	222_K	2.498	1.00
310_V	314_N	2.497	1.00
214_T	217_Q	2.484	1.00
80_L	89_T	2.447	1.00
5_L	9_I	2.412	1.00
89_T	94_K	2.397	1.00
90_I	98_L	2.373	1.00
51_A	80_L	2.366	1.00
100_R	120_I	2.301	1.00
101_F	105_F	2.283	1.00
342_W	346_W	2.242	1.00
85_E	89_T	2.229	1.00
265_L	352_T	2.220	1.00
273_L	358_A	2.216	1.00
260_M	324_F	2.184	1.00
235_T	257_Y	2.166	1.00
239_A	243_W	2.103	1.00
346_W	350_V	2.103	1.00
54_D	57_N	2.076	1.00
52_I	65_T	2.055	1.00
262_I	349_L	2.028	1.00
263_Y	324_F	2.019	1.00
83_P	100_R	1.986	1.00
266_S	352_T	1.977	1.00
55_E	83_P	1.973	1.00
54_D	61_S	1.961	1.00
350_V	354_T	1.945	1.00
81_K	85_E	1.907	1.00
55_E	100_R	1.904	1.00
14_Q	17_L	1.850	1.00
316_T	322_R	1.835	1.00
351_I	355_T	1.801	1.00
337_S	340_I	1.758	1.00
88_P	91_D	1.749	1.00
53_Y	86_I	1.724	1.00
269_G	352_T	1.721	1.00
58_G	61_S	1.715	1.00
255_L	331_I	1.711	1.00
234_A	260_M	1.695	1.00
6_W	10_R	1.686	1.00
47_N	75_T	1.681	1.00
227_L	261_V	1.671	1.00
262_I	352_T	1.661	1.00
56_D	106_S	1.655	1.00
326_D	344_S	1.624	1.00
254_A	258_F	1.617	1.00
199_E	222_K	1.610	1.00
49_T	77_V	1.598	1.00
14_Q	18_R	1.584	1.00
54_D	58_G	1.578	1.00
11_K	199_E	1.552	1.00
95_A	98_L	1.546	1.00
263_Y	267_L	1.537	1.00
227_L	265_L	1.529	1.00
317_W	323_H	1.529	1.00
230_A	264_G	1.514	1.00
49_T	75_T	1.514	1.00
317_W	322_R	1.502	1.00
270_F	291_F	1.493	1.00
305_V	316_T	1.486	1.00
13_L	232_F	1.483	1.00
60_H	106_S	1.465	1.00
58_G	106_S	1.463	1.00
170_D	173_W	1.463	1.00
84_Q	87_R	1.462	1.00
179_L	182_M	1.448	1.00
128_S	131_I	1.438	1.00
5_L	217_Q	1.437	1.00
60_H	109_L	1.430	1.00
266_S	355_T	1.396	1.00
280_T	283_Q	1.389	1.00
259_T	345_L	1.382	1.00
347_P	351_I	1.374	1.00
55_E	103_A	1.367	1.00
262_I	345_L	1.365	1.00
343_N	347_P	1.365	1.00
276_S	362_M	1.361	1.00
193_S	284_A	1.349	1.00
63_E	66_Q	1.347	1.00
67_R	70_R	1.339	1.00
61_S	106_S	1.333	1.00
66_Q	69_A	1.332	1.00
357_S	361_A	1.332	1.00
85_E	88_P	1.313	1.00
87_R	120_I	1.300	1.00
231_T	261_V	1.294	1.00
273_L	359_A	1.294	1.00
239_A	242_I	1.292	1.00
104_D	107_R	1.291	1.00
140_V	144_Q	1.280	1.00
313_Q	317_W	1.279	1.00
330_Q	336_A	1.279	1.00
56_D	104_D	1.277	1.00
310_V	313_Q	1.272	1.00
100_R	118_Q	1.268	1.00
216_W	360_Y	1.260	1.00
68_F	136_L	1.259	1.00
322_R	326_D	1.251	1.00
192_T	196_V	1.242	1.00
311_W	314_N	1.239	1.00
51_A	89_T	1.237	1.00
137_Q	141_K	1.232	1.00
252_S	255_L	1.232	1.00
9_I	221_G	1.226	1.00
13_L	228_I	1.226	1.00
240_I	244_A	1.225	1.00
5_L	220_I	1.217	1.00
314_N	318_I	1.216	1.00
128_S	132_A	1.211	1.00
259_T	331_I	1.203	1.00
330_Q	334_K	1.201	1.00
17_L	20_P	1.199	1.00
216_W	220_I	1.195	1.00
347_P	350_V	1.194	1.00
30_V	40_A	1.190	1.00
345_L	349_L	1.184	1.00
97_L	132_A	1.181	1.00
323_H	347_P	1.174	1.00
9_I	225_P	1.173	1.00
90_I	95_A	1.169	1.00
83_P	98_L	1.168	1.00
311_W	315_L	1.167	1.00
135_Y	139_I	1.156	1.00
289_F	293_M	1.150	1.00
266_S	348_L	1.146	1.00
133_A	137_Q	1.142	1.00
314_N	317_W	1.135	1.00
56_D	101_F	1.133	1.00
271_G	275_S	1.132	1.00
136_L	139_I	1.130	1.00
219_F	360_Y	1.128	1.00
53_Y	80_L	1.125	1.00
293_M	296_I	1.124	1.00
266_S	351_I	1.123	1.00
217_Q	221_G	1.122	1.00
106_S	110_D	1.121	1.00
309_P	313_Q	1.116	1.00
273_L	362_M	1.115	1.00
228_I	232_F	1.113	1.00
6_W	9_I	1.108	1.00
5_L	221_G	1.101	1.00
238_L	260_M	1.098	1.00
319_N	322_R	1.094	1.00
197_A	200_R	1.080	1.00
35_I	39_F	1.052	1.00
199_E	204_T	1.050	1.00
305_V	308_M	1.050	1.00
84_Q	88_P	1.040	1.00
162_R	165_Y	1.033	1.00
323_H	344_S	1.026	1.00
50_I	99_V	1.024	1.00
221_G	225_P	1.020	1.00
98_L	120_I	1.016	1.00
181_A	324_F	1.008	1.00
256_F	328_T	1.008	1.00
308_M	313_Q	1.008	1.00
130_Q	133_A	1.006	1.00
8_L	213_L	0.994	1.00
141_K	145_Q	0.991	1.00
254_A	257_Y	0.990	1.00
138_Q	142_N	0.984	1.00
197_A	284_A	0.983	1.00
264_G	268_V	0.983	1.00
177_P	181_A	0.982	1.00
81_K	89_T	0.981	1.00
269_G	356_G	0.972	1.00
273_L	355_T	0.964	1.00
49_T	96_L	0.961	1.00
34_V	38_P	0.954	1.00
80_L	95_A	0.954	1.00
180_I	188_V	0.952	1.00
182_M	188_V	0.948	1.00
354_T	358_A	0.947	1.00
19_E	22_T	0.943	1.00
177_P	182_M	0.941	1.00
53_Y	98_L	0.937	1.00
335_D	338_L	0.932	1.00
336_A	340_I	0.929	1.00
11_K	14_Q	0.929	1.00
34_V	37_F	0.927	1.00
62_V	66_Q	0.927	1.00
238_L	256_F	0.924	1.00
34_V	241_G	0.919	1.00
352_T	356_G	0.913	1.00
339_D	343_N	0.910	1.00
231_T	235_T	0.899	1.00
290_V	294_P	0.899	1.00
300_G	304_P	0.898	1.00
99_V	119_L	0.896	1.00
154_P	157_S	0.895	1.00
255_L	258_F	0.889	1.00
35_I	240_I	0.887	1.00
61_S	101_F	0.886	1.00
349_L	353_A	0.881	1.00
61_S	65_T	0.879	1.00
326_D	330_Q	0.875	1.00
223_A	268_V	0.873	1.00
81_K	86_I	0.871	1.00
13_L	225_P	0.869	1.00
61_S	64_L	0.854	1.00
269_G	355_T	0.854	1.00
57_N	103_A	0.853	1.00
355_T	359_A	0.849	1.00
227_L	268_V	0.848	1.00
135_Y	138_Q	0.847	1.00
50_I	97_L	0.844	1.00
122_D	125_N	0.844	1.00
65_T	69_A	0.832	1.00
132_A	135_Y	0.832	1.00
197_A	201_E	0.830	1.00
309_P	312_L	0.829	1.00
119_L	122_D	0.828	1.00
73_A	77_V	0.828	1.00
352_T	355_T	0.827	1.00
260_M	328_T	0.827	1.00
286_I	289_F	0.826	1.00
13_L	17_L	0.824	1.00
185_T	267_L	0.823	1.00
33_Q	37_F	0.820	1.00
278_C	287_G	0.819	1.00
344_S	348_L	0.817	1.00
184_T	188_V	0.815	1.00
270_F	355_T	0.813	1.00
323_H	326_D	0.812	1.00
86_I	89_T	0.812	1.00
223_A	265_L	0.811	1.00
112_F	115_A	0.808	1.00
12_E	225_P	0.806	1.00
99_V	117_L	0.801	1.00
182_M	186_I	0.801	1.00
208_L	218_I	0.801	1.00
77_V	81_K	0.801	1.00
273_L	277_L	0.800	1.00
83_P	86_I	0.799	1.00
253_L	257_Y	0.799	1.00
81_K	95_A	0.797	1.00
185_T	188_V	0.796	1.00
296_I	299_S	0.793	1.00
278_C	283_Q	0.788	1.00
292_M	296_I	0.787	1.00
30_V	33_Q	0.787	1.00
341_V	345_L	0.786	1.00
198_R	202_Q	0.783	1.00
31_L	35_I	0.782	1.00
196_V	199_E	0.775	1.00
178_S	183_I	0.775	1.00
80_L	86_I	0.772	1.00
348_L	351_I	0.770	1.00
187_G	233_Q	0.768	1.00
176_V	179_L	0.764	1.00
63_E	67_R	0.763	1.00
259_T	341_V	0.763	1.00
54_D	65_T	0.757	1.00
156_N	159_L	0.756	1.00
82_S	86_I	0.755	1.00
156_N	161_V	0.754	1.00
200_R	203_G	0.752	1.00
118_Q	121_L	0.751	1.00
30_V	36_L	0.751	1.00
183_I	188_V	0.751	1.00
56_D	61_S	0.750	1.00
199_E	203_G	0.750	1.00
276_S	359_A	0.745	1.00
316_T	319_N	0.743	1.00
96_L	122_D	0.738	1.00
36_L	39_F	0.737	1.00
71_A	74_F	0.737	1.00
69_A	76_H	0.736	1.00
178_S	181_A	0.734	1.00
213_L	218_I	0.733	1.00
343_N	350_V	0.732	1.00
224_V	228_I	0.731	1.00
153_K	156_N	0.731	1.00
64_L	105_F	0.726	1.00
223_A	269_G	0.726	1.00
73_A	76_H	0.725	1.00
181_A	188_V	0.721	1.00
181_A	321_I	0.721	1.00
51_A	98_L	0.718	1.00
201_E	281_Q	0.717	1.00
141_K	144_Q	0.716	1.00
155_N	158_E	0.714	1.00
174_F	188_V	0.712	1.00
54_D	101_F	0.712	1.00
205_L	218_I	0.711	1.00
305_V	313_Q	0.710	1.00
132_A	140_V	0.705	1.00
330_Q	344_S	0.703	1.00
262_I	348_L	0.697	1.00
286_I	295_A	0.696	1.00
9_I	13_L	0.696	1.00
272_L	359_A	0.693	1.00
11_K	15_S	0.691	1.00
356_G	360_Y	0.690	1.00
344_S	347_P	0.688	1.00
323_H	351_I	0.686	1.00
194_L	197_A	0.686	1.00
87_R	98_L	0.686	1.00
64_L	101_F	0.686	1.00
344_S	351_I	0.685	1.00
97_L	136_L	0.683	1.00
257_Y	260_M	0.682	1.00
159_L	162_R	0.681	1.00
209_L	218_I	0.676	1.00
340_I	343_N	0.675	1.00
53_Y	56_D	0.674	1.00
80_L	83_P	0.674	1.00
161_V	164_W	0.674	1.00
320_P	332_Y	0.666	1.00
133_A	136_L	0.663	1.00
308_M	312_L	0.663	1.00
24_A	28_L	0.662	1.00
7_T	10_R	0.657	1.00
291_F	295_A	0.657	1.00
255_L	341_V	0.654	1.00
246_Q	249_F	0.654	1.00
53_Y	82_S	0.650	1.00
273_L	276_S	0.650	1.00
222_K	226_A	0.649	1.00
52_I	55_E	0.647	1.00
71_A	76_H	0.647	1.00
89_T	92_T	0.646	1.00
274_I	278_C	0.642	1.00
349_L	352_T	0.641	1.00
12_E	16_L	0.641	1.00
60_H	63_E	0.639	1.00
8_L	218_I	0.634	1.00
121_L	129_A	0.633	1.00
324_F	327_I	0.633	1.00
192_T	199_E	0.631	1.00
38_P	245_Y	0.631	1.00
60_H	65_T	0.630	1.00
131_I	135_Y	0.629	1.00
200_R	205_L	0.627	1.00
5_L	216_W	0.627	1.00
196_V	200_R	0.626	1.00
175_V	179_L	0.626	1.00
355_T	358_A	0.625	1.00
191_V	195_S	0.622	1.00
105_F	115_A	0.620	1.00
219_F	272_L	0.619	1.00
330_Q	340_I	0.618	1.00
177_P	184_T	0.617	1.00
233_Q	237_V	0.617	1.00
30_V	284_A	0.616	0.99
160_V	163_N	0.614	0.99
129_A	135_Y	0.614	0.99
90_I	93_Q	0.614	0.99
286_I	294_P	0.614	0.99
157_S	161_V	0.613	0.99
255_L	345_L	0.613	0.99
52_I	76_H	0.612	0.99
327_I	331_I	0.611	0.99
287_G	294_P	0.610	0.99
195_S	199_E	0.610	0.99
343_N	346_W	0.610	0.99
77_V	80_L	0.609	0.99
338_L	342_W	0.608	0.99
238_L	253_L	0.608	0.99
227_L	231_T	0.607	0.99
116_P	160_V	0.606	0.99
134_N	138_Q	0.606	0.99
327_I	330_Q	0.605	0.99
176_V	187_G	0.603	0.99
39_F	244_A	0.603	0.99
347_P	354_T	0.599	0.99
26_L	29_P	0.599	0.99
130_Q	134_N	0.598	0.99
295_A	319_N	0.598	0.99
294_P	297_L	0.596	0.99
346_W	349_L	0.596	0.99
183_I	187_G	0.596	0.99
347_P	355_T	0.595	0.99
7_T	11_K	0.595	0.99
329_K	332_Y	0.594	0.99
74_F	77_V	0.594	0.99
342_W	345_L	0.593	0.99
132_A	139_I	0.588	0.99
27_I	232_F	0.588	0.99
192_T	226_A	0.587	0.99
77_V	95_A	0.587	0.99
64_L	140_V	0.586	0.99
358_A	362_M	0.586	0.99
132_A	136_L	0.584	0.99
135_Y	140_V	0.584	0.99
208_L	211_S	0.581	0.99
105_F	143_Y	0.581	0.99
172_K	176_V	0.580	0.99
86_I	97_L	0.579	0.99
305_V	322_R	0.579	0.99
20_P	23_R	0.578	0.99
134_N	139_I	0.578	0.99
194_L	281_Q	0.578	0.99
235_T	238_L	0.577	0.99
37_F	41_A	0.574	0.99
340_I	344_S	0.573	0.99
182_M	187_G	0.573	0.99
198_R	201_E	0.573	0.99
353_A	357_S	0.573	0.99
16_L	26_L	0.573	0.99
72_S	75_T	0.572	0.99
16_L	229_V	0.570	0.99
83_P	120_I	0.569	0.99
336_A	341_V	0.568	0.99
232_F	235_T	0.568	0.99
29_P	33_Q	0.567	0.99
11_K	204_T	0.567	0.99
158_E	161_V	0.566	0.99
59_E	106_S	0.565	0.99
257_Y	261_V	0.565	0.99
179_L	185_T	0.565	0.99
174_F	184_T	0.563	0.99
86_I	90_I	0.562	0.99
52_I	56_D	0.561	0.99
223_A	272_L	0.561	0.99
177_P	187_G	0.560	0.99
176_V	188_V	0.560	0.99
283_Q	286_I	0.559	0.99
188_V	267_L	0.559	0.99
45_V	48_A	0.558	0.99
235_T	253_L	0.558	0.99
25_I	29_P	0.553	0.99
303_S	307_N	0.553	0.99
269_G	359_A	0.552	0.99
185_T	263_Y	0.552	0.99
192_T	195_S	0.551	0.99
102_P	116_P	0.551	0.99
321_I	325_T	0.550	0.99
128_S	139_I	0.550	0.99
249_F	253_L	0.548	0.99
116_P	158_E	0.548	0.99
161_V	165_Y	0.547	0.99
139_I	144_Q	0.545	0.99
108_K	115_A	0.545	0.99
139_I	143_Y	0.544	0.99
275_S	286_I	0.544	0.99
131_I	144_Q	0.544	0.99
319_N	323_H	0.543	0.99
327_I	336_A	0.542	0.99
289_F	292_M	0.541	0.99
219_F	356_G	0.541	0.99
175_V	188_V	0.540	0.99
223_A	227_L	0.540	0.99
327_I	341_V	0.539	0.99
30_V	34_V	0.538	0.99
154_P	159_L	0.538	0.99
163_N	167_P	0.538	0.99
62_V	65_T	0.538	0.99
108_K	116_P	0.537	0.99
34_V	237_V	0.537	0.99
261_V	265_L	0.535	0.99
168_N	173_W	0.535	0.99
160_V	164_W	0.534	0.99
353_A	356_G	0.533	0.99
97_L	119_L	0.533	0.99
292_M	295_A	0.532	0.99
34_V	40_A	0.530	0.98
297_L	303_S	0.529	0.98
338_L	341_V	0.529	0.98
328_T	332_Y	0.528	0.98
90_I	120_I	0.528	0.98
292_M	297_L	0.528	0.98
234_A	238_L	0.528	0.98
153_K	157_S	0.528	0.98
173_W	248_P	0.528	0.98
356_G	359_A	0.527	0.98
132_A	141_K	0.527	0.98
181_A	185_T	0.526	0.98
57_N	61_S	0.526	0.98
213_L	217_Q	0.525	0.98
327_I	348_L	0.525	0.98
155_N	159_L	0.524	0.98
351_I	354_T	0.524	0.98
30_V	37_F	0.524	0.98
327_I	344_S	0.523	0.98
181_A	184_T	0.522	0.98
12_E	218_I	0.521	0.98
35_I	38_P	0.521	0.98
221_G	224_V	0.521	0.98
88_P	94_K	0.521	0.98
258_F	262_I	0.521	0.98
135_Y	142_N	0.520	0.98
282_Q	286_I	0.520	0.98
101_F	117_L	0.519	0.98
50_I	55_E	0.517	0.98
28_L	32_I	0.517	0.98
107_R	111_T	0.514	0.98
339_D	342_W	0.513	0.98
317_W	320_P	0.513	0.98
266_S	270_F	0.513	0.98
171_Y	175_V	0.511	0.98
218_I	221_G	0.510	0.98
29_P	34_V	0.509	0.98
159_L	165_Y	0.508	0.98
204_T	212_P	0.508	0.98
175_V	178_S	0.505	0.98
51_A	55_E	0.504	0.98
140_V	145_Q	0.504	0.98
178_S	184_T	0.503	0.98
12_E	15_S	0.502	0.98
171_Y	174_F	0.502	0.98
60_H	143_Y	0.502	0.98
173_W	181_A	0.502	0.98
50_I	74_F	0.501	0.98
58_G	104_D	0.500	0.98
358_A	361_A	0.500	0.98
269_G	276_S	0.500	0.98

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
3cniA	2	0.3696	99.6	0.709	Contact Map
2p0sA	2	0.3288	97.7	0.852	Contact Map
2qv0A	2	0.3098	13.7	0.951	Contact Map
3gt7A	1	0.2826	13.3	0.951	Contact Map
3cnbA	1	0.3071	12.7	0.952	Contact Map
3cg4A	1	0.3125	11.5	0.953	Contact Map
3i6vA	1	0.4103	11.3	0.953	Contact Map
4le1A	2	0.3397	11.3	0.953	Contact Map
2gkgA	1	0.3016	10.8	0.953	Contact Map
3cg0A	4	0.3125	10.7	0.953	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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