YHDY - ECOLI - GREMLIN Contacts

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YHDY - Inner membrane amino-acid ABC transporter permease protein YhdY

UniProt:	P45768	Sequences: MTKVLLSHPPRPASHNSSRAMVWVRKNLFSSWSNSLLTIGCIWLMWELIPPLLNWAFLQANWVGSTRADCTKAGACWVFIHERFGQFMYGLYPHDQRWRINLALLIGLVSIAPMFWKILPHRGRYIAAWAVIYPLIVWWLMYGGFFALERVETRQWGGLTLTLIIASVGIAGALPWGILLALGRRSHMPIVRILSVIFIEFWRGVPLITVLFMSSVMLPLFMAEGTSIDKLIRALVGVILFQSAYVAEVVRGGLQALPKGQYEAAESLALGYWKTQGLVILPQALKLVIPGLVNTIIALFKDTSLVIIIGLFDLFSSVQQATVDPAWLGMSTEGYVFAALIYWIFCFSMSRYSQYLEKRFNTGRTPH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12836
Length:	367 (344)
Sequences:	927 (607)
Seq/√Len:	32.7

ECOLI - YHDY YHDX

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
183_G	195_S	5.885	1.00
53_L	58_L	5.352	1.00
266_E	275_T	4.960	1.00
54_N	59_Q	4.924	1.00
89_Y	101_N	4.810	1.00
30_S	34_N	4.710	1.00
318_V	334_G	3.699	1.00
161_L	311_L	3.266	1.00
85_G	97_R	3.178	1.00
165_I	238_V	3.152	1.00
300_F	345_F	2.968	1.00
23_W	27_N	2.795	1.00
52_L	56_A	2.779	1.00
43_W	47_E	2.696	1.00
169_G	299_L	2.668	1.00
32_W	36_L	2.629	1.00
35_S	39_I	2.613	1.00
262_Y	280_I	2.596	1.00
159_L	341_I	2.550	1.00
246_V	292_L	2.529	1.00
286_K	362_T	2.519	1.00
271_G	274_K	2.514	1.00
306_V	313_D	2.317	0.99
286_K	364_R	2.195	0.99
329_G	333_E	2.158	0.99
32_W	35_S	2.136	0.99
347_F	351_R	2.133	0.99
210_V	237_G	2.104	0.98
314_L	341_I	2.101	0.98
192_R	196_V	2.026	0.98
221_F	349_M	2.009	0.98
140_L	143_G	2.008	0.98
235_L	239_I	1.991	0.98
249_V	295_T	1.979	0.98
23_W	28_L	1.943	0.97
39_I	43_W	1.931	0.97
256_A	287_L	1.914	0.97
295_T	298_A	1.882	0.97
230_K	309_I	1.874	0.97
83_R	324_D	1.854	0.96
37_L	41_C	1.851	0.96
176_W	240_L	1.842	0.96
301_K	304_S	1.840	0.96
351_R	354_Q	1.832	0.96
20_A	24_V	1.797	0.96
43_W	46_W	1.792	0.96
318_V	338_A	1.765	0.95
293_V	302_D	1.752	0.95
55_W	333_E	1.749	0.95
264_A	267_S	1.728	0.95
126_I	130_A	1.710	0.94
33_S	36_L	1.707	0.94
45_M	50_P	1.706	0.94
86_Q	317_S	1.693	0.94
180_L	199_I	1.685	0.94
300_F	349_M	1.673	0.94
29_F	35_S	1.673	0.94
156_W	219_P	1.670	0.94
42_I	46_W	1.667	0.94
90_G	99_R	1.652	0.93
242_Q	298_A	1.645	0.93
84_F	88_M	1.632	0.93
67_R	71_T	1.631	0.93
64_G	78_V	1.615	0.92
44_L	47_E	1.604	0.92
222_M	225_G	1.599	0.92
250_V	285_L	1.588	0.92
166_A	267_S	1.580	0.92
92_Y	99_R	1.573	0.91
24_V	29_F	1.558	0.91
65_S	69_D	1.546	0.91
174_L	246_V	1.535	0.90
67_R	70_C	1.523	0.90
262_Y	275_T	1.515	0.90
249_V	294_N	1.473	0.88
64_G	69_D	1.472	0.88
162_T	314_L	1.457	0.88
178_I	250_V	1.452	0.88
141_M	156_W	1.442	0.87
79_F	321_A	1.428	0.87
42_I	176_W	1.416	0.86
61_N	78_V	1.404	0.86
333_E	356_L	1.384	0.85
89_Y	100_I	1.384	0.85
293_V	353_S	1.366	0.84
205_V	213_M	1.363	0.84
139_W	145_F	1.363	0.84
53_L	57_F	1.363	0.84
87_F	317_S	1.360	0.84
264_A	274_K	1.346	0.83
294_N	304_S	1.337	0.83
169_G	313_D	1.320	0.82
352_Y	355_Y	1.306	0.81
26_K	39_I	1.306	0.81
20_A	52_L	1.303	0.81
133_Y	137_V	1.302	0.81
292_L	299_L	1.287	0.81
20_A	23_W	1.282	0.80
289_I	353_S	1.280	0.80
272_Y	352_Y	1.268	0.80
40_G	48_L	1.263	0.79
161_L	329_G	1.259	0.79
165_I	306_V	1.242	0.78
159_L	314_L	1.239	0.78
96_Q	149_E	1.233	0.78
179_L	294_N	1.231	0.77
31_S	35_S	1.228	0.77
192_R	325_P	1.226	0.77
199_I	247_A	1.220	0.77
54_N	58_L	1.220	0.77
237_G	243_S	1.215	0.76
173_A	242_Q	1.210	0.76
51_P	54_N	1.209	0.76
304_S	314_L	1.207	0.76
176_W	243_S	1.207	0.76
41_C	45_M	1.204	0.76
64_G	71_T	1.198	0.75
114_M	120_P	1.196	0.75
64_G	79_F	1.191	0.75
155_Q	280_I	1.182	0.74
176_W	232_I	1.174	0.74
100_I	160_T	1.173	0.74
265_A	275_T	1.169	0.74
240_L	285_L	1.164	0.73
118_I	122_R	1.159	0.73
87_F	141_M	1.158	0.73
36_L	40_G	1.155	0.73
177_G	246_V	1.155	0.73
168_V	235_L	1.141	0.72
347_F	354_Q	1.131	0.71
79_F	334_G	1.126	0.71
105_L	146_F	1.126	0.71
314_L	338_A	1.123	0.71
124_R	128_A	1.122	0.71
162_T	342_Y	1.117	0.70
109_V	358_K	1.113	0.70
198_F	243_S	1.109	0.70
296_I	302_D	1.108	0.70
225_G	228_I	1.108	0.70
177_G	250_V	1.105	0.69
142_Y	150_R	1.094	0.69
79_F	83_R	1.094	0.69
215_S	230_K	1.093	0.68
27_N	32_W	1.090	0.68
234_A	309_I	1.089	0.68
205_V	209_T	1.087	0.68
197_I	201_F	1.079	0.67
92_Y	98_W	1.077	0.67
96_Q	99_R	1.067	0.67
193_I	197_I	1.066	0.67
291_G	294_N	1.054	0.66
37_L	190_I	1.051	0.65
51_P	59_Q	1.049	0.65
95_D	149_E	1.048	0.65
168_V	172_G	1.044	0.65
106_I	354_Q	1.038	0.64
211_L	305_L	1.038	0.64
87_F	335_Y	1.034	0.64
322_T	335_Y	1.034	0.64
198_F	244_A	1.031	0.64
59_Q	132_I	1.024	0.63
106_I	133_Y	1.022	0.63
190_I	194_L	1.019	0.63
22_V	26_K	1.016	0.63
170_I	299_L	1.012	0.62
141_M	145_F	1.008	0.62
144_G	148_L	1.007	0.62
159_L	162_T	0.990	0.61
204_G	302_D	0.989	0.61
274_K	277_G	0.989	0.61
288_V	304_S	0.983	0.60
30_S	35_S	0.971	0.59
288_V	291_G	0.963	0.59
249_V	291_G	0.962	0.58
88_M	104_L	0.961	0.58
173_A	239_I	0.961	0.58
128_A	132_I	0.958	0.58
97_R	101_N	0.951	0.58
141_M	164_I	0.948	0.57
153_T	231_L	0.947	0.57
289_I	313_D	0.940	0.57
41_C	46_W	0.939	0.57
112_A	116_W	0.936	0.56
153_T	229_D	0.932	0.56
267_S	274_K	0.932	0.56
170_I	297_I	0.929	0.56
32_W	38_T	0.928	0.56
228_I	232_I	0.927	0.56
136_I	140_L	0.922	0.55
272_Y	276_Q	0.921	0.55
289_I	356_L	0.920	0.55
308_I	313_D	0.913	0.54
41_C	50_P	0.912	0.54
230_K	319_Q	0.908	0.54
213_M	308_I	0.907	0.54
252_G	301_K	0.900	0.53
169_G	235_L	0.895	0.53
65_S	68_A	0.891	0.53
103_A	110_S	0.889	0.52
216_V	335_Y	0.887	0.52
83_R	174_L	0.881	0.52
293_V	360_F	0.881	0.52
49_I	53_L	0.874	0.51
140_L	145_F	0.874	0.51
257_L	280_I	0.872	0.51
161_L	333_E	0.869	0.51
289_I	293_V	0.868	0.51
26_K	46_W	0.865	0.50
20_A	26_K	0.859	0.50
354_Q	358_K	0.849	0.49
128_A	280_I	0.844	0.49
202_W	210_V	0.838	0.48
169_G	238_V	0.835	0.48
267_S	311_L	0.834	0.48
230_K	234_A	0.832	0.48
244_A	305_L	0.832	0.48
302_D	353_S	0.832	0.48
21_M	24_V	0.831	0.48
79_F	324_D	0.831	0.48
83_R	86_Q	0.828	0.47
46_W	50_P	0.821	0.47
219_P	237_G	0.820	0.47
90_G	93_P	0.819	0.47
40_G	44_L	0.817	0.46
61_N	72_K	0.817	0.46
242_Q	309_I	0.817	0.46
91_L	155_Q	0.816	0.46
34_N	46_W	0.816	0.46
90_G	98_W	0.815	0.46
270_L	274_K	0.814	0.46
58_L	65_S	0.809	0.46
93_P	98_W	0.808	0.46
212_F	252_G	0.800	0.45
285_L	342_Y	0.798	0.45
297_I	349_M	0.797	0.45
45_M	56_A	0.794	0.45
273_W	276_Q	0.791	0.44
156_W	230_K	0.788	0.44
315_F	335_Y	0.783	0.44
24_V	41_C	0.779	0.43
201_F	209_T	0.774	0.43
50_P	54_N	0.774	0.43
30_S	43_W	0.769	0.43
232_I	257_L	0.768	0.42
47_E	50_P	0.768	0.42
262_Y	266_E	0.766	0.42
21_M	25_R	0.766	0.42
142_Y	145_F	0.763	0.42
22_V	25_R	0.761	0.42
343_W	347_F	0.761	0.42
110_S	164_I	0.759	0.42
80_I	171_A	0.759	0.42
77_W	90_G	0.756	0.42
242_Q	295_T	0.754	0.41
326_A	348_S	0.754	0.41
196_V	199_I	0.753	0.41
31_S	345_F	0.753	0.41
64_G	67_R	0.752	0.41
61_N	73_A	0.751	0.41
33_S	37_L	0.751	0.41
70_C	301_K	0.751	0.41
118_I	121_H	0.750	0.41
108_L	112_A	0.748	0.41
307_I	312_F	0.747	0.41
32_W	179_L	0.745	0.41
23_W	32_W	0.743	0.40
43_W	202_W	0.742	0.40
316_S	320_Q	0.739	0.40
39_I	225_G	0.738	0.40
302_D	305_L	0.737	0.40
130_A	134_P	0.735	0.40
108_L	225_G	0.734	0.40
95_D	99_R	0.732	0.40
134_P	143_G	0.731	0.40
361_N	364_R	0.728	0.39
294_N	354_Q	0.728	0.39
42_I	50_P	0.728	0.39
36_L	80_I	0.727	0.39
245_Y	253_G	0.727	0.39
178_I	281_L	0.726	0.39
60_A	80_I	0.726	0.39
345_F	349_M	0.726	0.39
114_M	130_A	0.725	0.39
38_T	45_M	0.724	0.39
125_Y	130_A	0.723	0.39
248_E	261_Q	0.723	0.39
293_V	300_F	0.722	0.39
70_C	76_C	0.720	0.39
45_M	73_A	0.719	0.39
320_Q	323_V	0.718	0.38
296_I	345_F	0.718	0.38
325_P	342_Y	0.716	0.38
267_S	307_I	0.713	0.38
40_G	149_E	0.713	0.38
207_L	241_F	0.712	0.38
288_V	301_K	0.712	0.38
26_K	139_W	0.711	0.38
248_E	251_R	0.711	0.38
180_L	243_S	0.710	0.38
122_R	195_S	0.706	0.38
172_G	239_I	0.704	0.37
170_I	270_L	0.704	0.37
249_V	301_K	0.703	0.37
26_K	30_S	0.700	0.37
219_P	255_Q	0.699	0.37
31_S	188_M	0.697	0.37
21_M	48_L	0.697	0.37
264_A	324_D	0.694	0.37
88_M	100_I	0.691	0.36
87_F	160_T	0.691	0.36
70_C	78_V	0.691	0.36
208_I	298_A	0.687	0.36
89_Y	120_P	0.686	0.36
44_L	49_I	0.683	0.36
175_P	199_I	0.680	0.36
246_V	295_T	0.678	0.35
71_T	329_G	0.677	0.35
199_I	255_Q	0.676	0.35
218_L	229_D	0.675	0.35
40_G	58_L	0.675	0.35
213_M	299_L	0.675	0.35
77_W	99_R	0.675	0.35
340_L	344_I	0.675	0.35
185_R	246_V	0.674	0.35
57_F	362_T	0.673	0.35
249_V	288_V	0.672	0.35
315_F	324_D	0.671	0.35
214_S	224_E	0.671	0.35
335_Y	339_A	0.670	0.35
46_W	326_A	0.669	0.35
40_G	163_L	0.669	0.35
166_A	339_A	0.665	0.34
227_S	308_I	0.665	0.34
113_P	125_Y	0.665	0.34
254_L	284_A	0.663	0.34
26_K	127_A	0.663	0.34
143_G	148_L	0.662	0.34
132_I	187_H	0.662	0.34
93_P	222_M	0.662	0.34
232_I	280_I	0.662	0.34
277_G	343_W	0.659	0.34
188_M	349_M	0.658	0.34
209_T	236_V	0.656	0.34
292_L	310_G	0.654	0.34
34_N	196_V	0.652	0.33
196_V	200_E	0.652	0.33
134_P	140_L	0.651	0.33
171_A	240_L	0.650	0.33
124_R	257_L	0.649	0.33
38_T	42_I	0.647	0.33
169_G	296_I	0.645	0.33
314_L	342_Y	0.640	0.33
22_V	53_L	0.640	0.33
205_V	221_F	0.640	0.33
193_I	259_K	0.639	0.32
164_I	257_L	0.639	0.32
43_W	57_F	0.639	0.32
208_I	302_D	0.638	0.32
304_S	342_Y	0.638	0.32
44_L	73_A	0.637	0.32
120_P	160_T	0.637	0.32
279_V	353_S	0.637	0.32
141_M	160_T	0.636	0.32
271_G	275_T	0.636	0.32
261_Q	282_P	0.635	0.32
321_A	334_G	0.631	0.32
43_W	48_L	0.631	0.32
155_Q	309_I	0.630	0.32
63_V	68_A	0.629	0.32
242_Q	299_L	0.629	0.32
168_V	237_G	0.628	0.32
230_K	299_L	0.628	0.32
110_S	304_S	0.626	0.32
109_V	129_W	0.626	0.32
62_W	67_R	0.624	0.31
209_T	213_M	0.624	0.31
127_A	131_V	0.624	0.31
213_M	216_V	0.622	0.31
328_L	333_E	0.621	0.31
36_L	348_S	0.617	0.31
276_Q	309_I	0.615	0.31
234_A	303_T	0.614	0.31
107_G	165_I	0.614	0.31
310_G	316_S	0.613	0.31
231_L	324_D	0.609	0.30
83_R	160_T	0.608	0.30
107_G	133_Y	0.608	0.30
210_V	219_P	0.607	0.30
244_A	289_I	0.607	0.30
131_V	135_L	0.602	0.30
228_I	326_A	0.601	0.30
24_V	36_L	0.601	0.30
350_S	353_S	0.601	0.30
343_W	357_E	0.600	0.30
45_M	115_F	0.596	0.29
300_F	337_F	0.593	0.29
54_N	187_H	0.593	0.29
109_V	238_V	0.593	0.29
130_A	140_L	0.592	0.29
321_A	356_L	0.591	0.29
169_G	309_I	0.591	0.29
189_P	193_I	0.589	0.29
160_T	165_I	0.589	0.29
198_F	304_S	0.588	0.29
114_M	174_L	0.587	0.29
218_L	358_K	0.585	0.29
41_C	198_F	0.585	0.29
207_L	302_D	0.585	0.29
214_S	301_K	0.584	0.29
100_I	277_G	0.584	0.29
87_F	97_R	0.583	0.29
80_I	148_L	0.580	0.28
78_V	82_E	0.578	0.28
160_T	209_T	0.578	0.28
173_A	333_E	0.577	0.28
83_R	91_L	0.577	0.28
105_L	135_L	0.576	0.28
30_S	267_S	0.576	0.28
195_S	276_Q	0.575	0.28
103_A	196_V	0.575	0.28
297_I	353_S	0.574	0.28
30_S	33_S	0.574	0.28
169_G	242_Q	0.573	0.28
250_V	284_A	0.572	0.28
49_I	197_I	0.572	0.28
215_S	327_W	0.570	0.28
26_K	132_I	0.569	0.28
44_L	58_L	0.568	0.28
40_G	43_W	0.567	0.27
251_R	261_Q	0.563	0.27
169_G	197_I	0.562	0.27
154_R	320_Q	0.562	0.27
133_Y	326_A	0.562	0.27
21_M	341_I	0.562	0.27
31_S	34_N	0.562	0.27
124_R	127_A	0.561	0.27
296_I	299_L	0.561	0.27
284_A	305_L	0.559	0.27
222_M	265_A	0.559	0.27
81_H	359_R	0.557	0.27
177_G	278_L	0.554	0.27
165_I	359_R	0.554	0.27
106_I	137_V	0.552	0.27
260_G	263_E	0.550	0.26
48_L	336_V	0.549	0.26
309_I	319_Q	0.548	0.26
103_A	107_G	0.547	0.26
89_Y	94_H	0.545	0.26
331_S	335_Y	0.544	0.26
184_R	200_E	0.540	0.26
289_I	349_M	0.540	0.26
42_I	68_A	0.539	0.26
209_T	279_V	0.539	0.26
239_I	324_D	0.538	0.26
136_I	139_W	0.537	0.26
168_V	340_L	0.537	0.26
162_T	341_I	0.536	0.25
183_G	189_P	0.536	0.25
106_I	109_V	0.536	0.25
164_I	354_Q	0.535	0.25
342_Y	356_L	0.534	0.25
297_I	305_L	0.534	0.25
278_L	289_I	0.533	0.25
216_V	230_K	0.532	0.25
300_F	350_S	0.532	0.25
358_K	363_G	0.532	0.25
31_S	59_Q	0.531	0.25
168_V	222_M	0.530	0.25
55_W	311_L	0.529	0.25
169_G	289_I	0.528	0.25
156_W	159_L	0.527	0.25
24_V	27_N	0.525	0.25
171_A	286_K	0.524	0.25
154_R	319_Q	0.524	0.25
207_L	237_G	0.524	0.25
248_E	282_P	0.523	0.25
156_W	220_L	0.522	0.25
304_S	340_L	0.522	0.25
108_L	201_F	0.521	0.25
243_S	315_F	0.521	0.25
45_M	145_F	0.521	0.25
264_A	333_E	0.521	0.25
34_N	289_I	0.519	0.24
157_G	233_R	0.518	0.24
88_M	102_L	0.518	0.24
103_A	128_A	0.518	0.24
164_I	302_D	0.518	0.24
37_L	67_R	0.517	0.24
167_S	171_A	0.516	0.24
135_L	279_V	0.516	0.24
315_F	338_A	0.516	0.24
236_V	276_Q	0.516	0.24
259_K	266_E	0.515	0.24
196_V	222_M	0.514	0.24
257_L	287_L	0.514	0.24
38_T	44_L	0.514	0.24
39_I	326_A	0.513	0.24
214_S	309_I	0.511	0.24
97_R	104_L	0.509	0.24
279_V	317_S	0.509	0.24
222_M	279_V	0.509	0.24
112_A	351_R	0.508	0.24
264_A	294_N	0.508	0.24
90_G	207_L	0.506	0.24
44_L	48_L	0.506	0.24
91_L	96_Q	0.505	0.24
52_L	57_F	0.503	0.23
21_M	68_A	0.503	0.23
40_G	51_P	0.503	0.23
238_V	313_D	0.503	0.23
319_Q	322_T	0.501	0.23
191_V	309_I	0.501	0.23
195_S	313_D	0.501	0.23
347_F	350_S	0.501	0.23
301_K	319_Q	0.500	0.23
277_G	280_I	0.500	0.23

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
4ymuD	2	0.5858	100	0.762	Contact Map
3tuiA	2	0.5695	99.9	0.788	Contact Map
2onkC	2	0.6649	99.9	0.799	Contact Map
3d31C	2	0.6376	99.9	0.801	Contact Map
3rlfF	1	0.8665	99.9	0.813	Contact Map
3rlfG	1	0.6975	99.8	0.819	Contact Map
4tquM	1	0.7003	99.8	0.82	Contact Map
4tquN	1	0.7139	99.7	0.844	Contact Map
2m7cA	1	0.0545	7.4	0.978	Contact Map
3mktA	1	0.2262	6.3	0.979	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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