YTRD - BACSU - GREMLIN Contacts

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YTRD - Probable ABC transporter permease YtrD

UniProt:	O34953	Sequences: MPDSGLLYKEWRQNKVALVITILVFILGNPLSILNMYLIYQGCVTGKENWVGPCVFSVDYLNSSFISLFWIWGVVLAVSQLGIERSKSFFDFTLSLPYTRGQIFHAKFLTGGMVIVVPQLIGYVLSVLLIMLLKPDQAVYFHNYSLGMIIVSMLAYSLVMAGGALTGNSFAQLLVSFTVAISPFLLISLPVINLEILFGGSIDFIHGPVPKWVQYFIPIIYVDSKWAENSPYYLVIPAIMTIIFYIIGYISFVKMSNERNGYFFLWKPLNRPVQIIVIIIGIMGFGYFGFTASESFAGYLIGMGTGAVIGFLISYFAIYKKMKLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	325 (311)
Sequences:	584 (479)
Seq/√Len:	27.2

BACSU - YTRD YTRC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
104_F	248_G	6.555	1.00
111_G	156_Y	4.441	1.00
10_E	107_K	4.207	1.00
116_V	149_I	3.890	1.00
108_F	157_S	3.888	1.00
26_I	122_G	3.612	1.00
240_M	244_F	3.603	1.00
84_E	255_M	3.515	1.00
274_Q	315_Y	3.446	1.00
302_G	306_G	3.263	1.00
85_R	163_G	3.247	1.00
105_H	245_Y	3.112	1.00
163_G	172_Q	3.000	1.00
285_F	302_G	2.833	1.00
150_I	241_T	2.769	1.00
94_L	252_F	2.751	1.00
90_F	257_N	2.669	0.99
273_V	279_I	2.637	0.99
101_G	249_Y	2.502	0.99
80_Q	156_Y	2.498	0.99
185_L	279_I	2.470	0.99
94_L	257_N	2.376	0.99
156_Y	166_T	2.367	0.99
112_G	116_V	2.353	0.99
101_G	253_V	2.323	0.98
81_L	160_M	2.306	0.98
121_I	124_V	2.125	0.97
100_R	103_I	2.084	0.97
178_T	279_I	2.040	0.96
83_I	118_P	1.990	0.96
282_I	285_F	1.966	0.96
167_G	261_G	1.948	0.95
9_K	84_E	1.946	0.95
84_E	107_K	1.942	0.95
178_T	273_V	1.941	0.95
158_L	186_L	1.925	0.95
83_I	255_M	1.913	0.95
104_F	166_T	1.909	0.95
19_V	75_V	1.887	0.94
99_T	253_V	1.884	0.94
281_G	307_A	1.870	0.94
82_G	172_Q	1.826	0.93
94_L	103_I	1.810	0.93
277_V	302_G	1.783	0.93
96_L	103_I	1.736	0.92
77_A	285_F	1.731	0.91
162_G	166_T	1.728	0.91
84_E	260_N	1.725	0.91
165_L	175_V	1.702	0.91
21_T	25_F	1.690	0.90
255_M	260_N	1.678	0.90
85_R	172_Q	1.632	0.89
68_L	153_M	1.622	0.88
297_A	301_I	1.615	0.88
7_L	110_T	1.595	0.88
313_I	317_A	1.580	0.87
247_I	254_K	1.531	0.85
108_F	156_Y	1.526	0.85
176_S	183_P	1.513	0.85
255_M	315_Y	1.508	0.84
215_Y	218_P	1.492	0.84
115_I	152_S	1.484	0.83
171_A	197_L	1.484	0.83
12_R	15_K	1.479	0.83
185_L	189_L	1.465	0.83
22_I	121_I	1.464	0.83
91_D	95_S	1.450	0.82
306_G	310_G	1.445	0.82
84_E	163_G	1.442	0.82
92_F	198_F	1.440	0.82
84_E	93_T	1.419	0.81
165_L	270_N	1.410	0.80
93_T	255_M	1.377	0.79
81_L	163_G	1.358	0.78
182_S	186_L	1.350	0.77
9_K	13_Q	1.345	0.77
177_F	310_G	1.342	0.77
217_I	220_I	1.340	0.77
91_D	263_F	1.336	0.76
149_I	238_A	1.325	0.76
94_L	315_Y	1.316	0.75
84_E	110_T	1.316	0.75
9_K	93_T	1.299	0.74
197_L	300_L	1.297	0.74
314_S	318_I	1.284	0.73
6_L	103_I	1.282	0.73
189_L	284_G	1.276	0.73
279_I	282_I	1.270	0.73
6_L	85_R	1.260	0.72
157_S	241_T	1.256	0.72
11_W	19_V	1.250	0.71
178_T	181_I	1.249	0.71
27_L	31_L	1.242	0.71
279_I	318_I	1.241	0.71
107_K	110_T	1.241	0.71
26_I	190_P	1.238	0.71
16_V	111_G	1.237	0.71
234_L	283_M	1.231	0.70
9_K	260_N	1.225	0.70
70_W	272_P	1.221	0.70
89_F	93_T	1.217	0.69
284_G	302_G	1.210	0.69
174_L	178_T	1.198	0.68
200_G	311_F	1.186	0.67
239_I	246_I	1.183	0.67
113_M	121_I	1.170	0.66
45_T	238_A	1.170	0.66
112_G	153_M	1.165	0.66
310_G	314_S	1.161	0.66
85_R	260_N	1.152	0.65
182_S	279_I	1.148	0.65
94_L	118_P	1.146	0.65
96_L	255_M	1.144	0.64
216_F	220_I	1.136	0.64
83_I	94_L	1.132	0.64
12_R	267_K	1.132	0.64
123_Y	145_S	1.130	0.63
39_I	242_I	1.129	0.63
161_A	244_F	1.126	0.63
259_R	270_N	1.121	0.63
83_I	93_T	1.118	0.63
152_S	165_L	1.107	0.62
82_G	169_S	1.107	0.62
15_K	18_L	1.105	0.62
92_F	110_T	1.103	0.61
40_Y	87_K	1.097	0.61
311_F	320_K	1.096	0.61
113_M	138_A	1.093	0.61
9_K	14_N	1.086	0.60
171_A	263_F	1.081	0.60
76_L	115_I	1.076	0.60
298_G	302_G	1.071	0.59
200_G	316_F	1.069	0.59
92_F	222_V	1.064	0.59
104_F	218_P	1.042	0.57
6_L	107_K	1.040	0.57
141_F	144_Y	1.036	0.57
239_I	243_I	1.031	0.56
146_L	150_I	1.023	0.56
75_V	184_F	1.020	0.55
5_G	14_N	1.020	0.55
171_A	261_G	1.018	0.55
125_L	233_Y	1.008	0.54
130_I	135_P	1.006	0.54
146_L	242_I	1.003	0.54
24_V	102_Q	1.003	0.54
103_I	107_K	0.993	0.53
147_G	234_L	0.987	0.53
84_E	263_F	0.983	0.53
23_L	256_S	0.979	0.52
13_Q	91_D	0.976	0.52
6_L	157_S	0.970	0.52
182_S	320_K	0.966	0.51
300_L	304_G	0.965	0.51
85_R	255_M	0.964	0.51
318_I	321_K	0.964	0.51
14_N	80_Q	0.959	0.51
316_F	320_K	0.954	0.50
16_V	180_A	0.949	0.50
280_I	284_G	0.946	0.50
162_G	179_V	0.945	0.50
9_K	91_D	0.941	0.49
309_I	317_A	0.938	0.49
94_L	97_P	0.936	0.49
48_E	146_L	0.935	0.49
6_L	93_T	0.927	0.48
133_L	165_L	0.923	0.48
30_P	310_G	0.922	0.48
103_I	252_F	0.922	0.48
82_G	85_R	0.920	0.48
111_G	252_F	0.919	0.48
77_A	159_V	0.917	0.48
98_Y	234_L	0.914	0.47
90_F	94_L	0.914	0.47
81_L	85_R	0.913	0.47
255_M	263_F	0.913	0.47
84_E	89_F	0.912	0.47
165_L	171_A	0.910	0.47
273_V	277_V	0.910	0.47
77_A	155_A	0.907	0.47
15_K	91_D	0.901	0.46
23_L	113_M	0.900	0.46
85_R	277_V	0.899	0.46
178_T	311_F	0.897	0.46
177_F	305_T	0.890	0.46
125_L	187_I	0.887	0.45
7_L	11_W	0.885	0.45
10_E	110_T	0.885	0.45
85_R	98_Y	0.883	0.45
97_P	287_Y	0.883	0.45
121_I	228_E	0.883	0.45
260_N	315_Y	0.881	0.45
107_K	260_N	0.875	0.44
276_I	310_G	0.875	0.44
24_V	116_V	0.871	0.44
201_S	304_G	0.867	0.44
27_L	301_I	0.867	0.44
165_L	251_S	0.859	0.43
161_A	178_T	0.858	0.43
281_G	287_Y	0.856	0.43
91_D	255_M	0.853	0.43
182_S	269_L	0.851	0.43
80_Q	115_I	0.849	0.43
185_L	284_G	0.843	0.42
87_K	171_A	0.839	0.42
99_T	249_Y	0.838	0.42
31_L	138_A	0.837	0.42
119_Q	145_S	0.836	0.42
152_S	321_K	0.836	0.42
8_Y	11_W	0.834	0.41
124_V	242_I	0.830	0.41
167_G	258_E	0.826	0.41
28_G	57_S	0.825	0.41
100_R	252_F	0.819	0.40
295_S	300_L	0.819	0.40
98_Y	305_T	0.819	0.40
42_G	124_V	0.815	0.40
195_E	278_I	0.814	0.40
87_K	91_D	0.813	0.40
81_L	164_A	0.811	0.40
178_T	269_L	0.805	0.39
10_E	84_E	0.805	0.39
146_L	234_L	0.804	0.39
15_K	180_A	0.804	0.39
132_L	186_L	0.803	0.39
9_K	263_F	0.803	0.39
161_A	255_M	0.803	0.39
255_M	265_L	0.797	0.39
11_W	275_I	0.796	0.39
39_I	251_S	0.794	0.39
253_V	257_N	0.794	0.39
238_A	293_S	0.790	0.38
190_P	194_L	0.790	0.38
193_N	197_L	0.787	0.38
133_L	307_A	0.787	0.38
26_I	292_A	0.784	0.38
256_S	259_R	0.781	0.38
94_L	255_M	0.779	0.37
234_L	238_A	0.776	0.37
144_Y	257_N	0.775	0.37
33_I	276_I	0.771	0.37
316_F	321_K	0.771	0.37
264_F	270_N	0.760	0.36
92_F	125_L	0.759	0.36
281_G	288_F	0.759	0.36
270_N	318_I	0.756	0.36
82_G	108_F	0.751	0.36
165_L	269_L	0.751	0.36
68_L	170_F	0.750	0.35
73_G	77_A	0.742	0.35
66_I	139_V	0.741	0.35
122_G	125_L	0.741	0.35
38_L	170_F	0.739	0.35
72_W	155_A	0.738	0.35
276_I	280_I	0.733	0.34
289_G	305_T	0.732	0.34
159_V	176_S	0.732	0.34
37_Y	242_I	0.731	0.34
116_V	177_F	0.731	0.34
11_W	134_K	0.730	0.34
17_A	116_V	0.730	0.34
288_F	302_G	0.729	0.34
200_G	320_K	0.728	0.34
76_L	104_F	0.726	0.34
33_I	281_G	0.721	0.33
191_V	205_I	0.718	0.33
186_L	309_I	0.717	0.33
128_L	235_V	0.716	0.33
80_Q	88_S	0.716	0.33
203_D	235_V	0.715	0.33
37_Y	133_L	0.712	0.33
211_K	304_G	0.711	0.33
21_T	84_E	0.710	0.33
282_I	311_F	0.705	0.32
91_D	262_Y	0.704	0.32
70_W	245_Y	0.700	0.32
310_G	316_F	0.697	0.32
127_V	304_G	0.695	0.32
174_L	273_V	0.695	0.32
109_L	239_I	0.692	0.32
161_A	251_S	0.692	0.32
75_V	228_E	0.691	0.31
55_V	58_V	0.691	0.31
129_L	231_P	0.684	0.31
104_F	108_F	0.680	0.31
179_V	185_L	0.679	0.31
71_I	276_I	0.678	0.31
17_A	165_L	0.678	0.31
160_M	184_F	0.676	0.30
31_L	133_L	0.675	0.30
259_R	262_Y	0.675	0.30
90_F	255_M	0.675	0.30
4_S	34_L	0.674	0.30
119_Q	137_Q	0.674	0.30
127_V	242_I	0.673	0.30
240_M	307_A	0.673	0.30
78_V	85_R	0.672	0.30
142_H	146_L	0.670	0.30
146_L	297_A	0.664	0.30
30_P	218_P	0.662	0.30
35_N	300_L	0.660	0.29
189_L	218_P	0.658	0.29
210_P	293_S	0.656	0.29
123_Y	141_F	0.650	0.29
81_L	98_Y	0.649	0.29
62_N	71_I	0.649	0.29
146_L	247_I	0.649	0.29
134_K	137_Q	0.646	0.29
73_G	100_R	0.644	0.28
113_M	238_A	0.641	0.28
99_T	212_W	0.639	0.28
27_L	305_T	0.638	0.28
46_G	239_I	0.636	0.28
196_I	256_S	0.634	0.28
183_P	279_I	0.630	0.28
118_P	121_I	0.630	0.28
99_T	201_S	0.630	0.28
72_W	195_E	0.629	0.28
97_P	118_P	0.629	0.28
301_I	317_A	0.627	0.27
200_G	237_P	0.627	0.27
156_Y	253_V	0.626	0.27
177_F	273_V	0.626	0.27
84_E	315_Y	0.624	0.27
148_M	308_V	0.623	0.27
259_R	264_F	0.623	0.27
103_I	273_V	0.620	0.27
93_T	107_K	0.617	0.27
162_G	302_G	0.616	0.27
25_F	119_Q	0.616	0.27
84_E	168_N	0.616	0.27
61_L	239_I	0.614	0.27
182_S	273_V	0.612	0.27
193_N	307_A	0.610	0.26
82_G	86_S	0.609	0.26
80_Q	183_P	0.604	0.26
93_T	260_N	0.602	0.26
185_L	271_R	0.602	0.26
159_V	163_G	0.601	0.26
73_G	255_M	0.601	0.26
170_F	266_W	0.601	0.26
177_F	219_I	0.600	0.26
264_F	273_V	0.599	0.26
268_P	313_I	0.599	0.26
199_G	222_V	0.599	0.26
75_V	113_M	0.596	0.26
26_I	309_I	0.596	0.26
43_C	248_G	0.594	0.26
108_F	222_V	0.592	0.25
34_L	234_L	0.590	0.25
236_I	313_I	0.590	0.25
32_S	117_V	0.590	0.25
131_M	243_I	0.589	0.25
113_M	227_A	0.589	0.25
66_I	72_W	0.587	0.25
73_G	162_G	0.587	0.25
70_W	196_I	0.586	0.25
280_I	283_M	0.585	0.25
18_L	284_G	0.584	0.25
44_V	77_A	0.583	0.25
177_F	300_L	0.583	0.25
235_V	308_V	0.582	0.25
80_Q	311_F	0.582	0.25
285_F	310_G	0.582	0.25
210_P	243_I	0.577	0.25
80_Q	107_K	0.576	0.24
97_P	264_F	0.574	0.24
267_K	296_F	0.573	0.24
26_I	252_F	0.573	0.24
43_C	128_L	0.569	0.24
165_L	268_P	0.566	0.24
242_I	254_K	0.566	0.24
277_V	281_G	0.566	0.24
172_Q	277_V	0.565	0.24
77_A	108_F	0.564	0.24
16_V	277_V	0.564	0.24
238_A	307_A	0.561	0.24
163_G	175_V	0.561	0.24
160_M	164_A	0.560	0.24
54_C	129_L	0.559	0.24
103_I	321_K	0.559	0.24
109_L	117_V	0.558	0.23
242_I	253_V	0.558	0.23
301_I	305_T	0.557	0.23
158_L	274_Q	0.556	0.23
280_I	310_G	0.555	0.23
240_M	291_T	0.555	0.23
211_K	225_K	0.553	0.23
126_S	129_L	0.552	0.23
15_K	262_Y	0.551	0.23
87_K	132_L	0.550	0.23
74_V	304_G	0.548	0.23
93_T	161_A	0.548	0.23
81_L	104_F	0.548	0.23
91_D	97_P	0.546	0.23
63_S	67_S	0.545	0.23
78_V	111_G	0.544	0.23
42_G	243_I	0.544	0.23
96_L	273_V	0.543	0.23
124_V	234_L	0.542	0.23
116_V	139_V	0.541	0.23
4_S	256_S	0.540	0.23
144_Y	156_Y	0.539	0.22
89_F	182_S	0.538	0.22
86_S	281_G	0.538	0.22
42_G	204_F	0.537	0.22
86_S	173_L	0.534	0.22
182_S	201_S	0.534	0.22
30_P	126_S	0.533	0.22
264_F	269_L	0.533	0.22
75_V	192_I	0.532	0.22
6_L	98_Y	0.532	0.22
59_D	227_A	0.530	0.22
123_Y	144_Y	0.529	0.22
85_R	107_K	0.529	0.22
21_T	30_P	0.529	0.22
238_A	268_P	0.527	0.22
140_Y	145_S	0.527	0.22
91_D	257_N	0.526	0.22
25_F	144_Y	0.526	0.22
47_K	239_I	0.524	0.22
143_N	246_I	0.524	0.22
183_P	305_T	0.524	0.22
175_V	311_F	0.524	0.22
157_S	245_Y	0.522	0.22
174_L	276_I	0.522	0.22
202_I	214_Q	0.522	0.22
80_Q	111_G	0.521	0.22
212_W	225_K	0.519	0.21
303_M	319_Y	0.519	0.21
67_S	113_M	0.519	0.21
213_V	235_V	0.518	0.21
85_R	92_F	0.517	0.21
82_G	299_Y	0.517	0.21
162_G	165_L	0.517	0.21
177_F	181_I	0.517	0.21
228_E	232_Y	0.515	0.21
68_L	276_I	0.514	0.21
279_I	311_F	0.513	0.21
245_Y	254_K	0.512	0.21
238_A	287_Y	0.512	0.21
193_N	301_I	0.512	0.21
194_L	305_T	0.511	0.21
130_I	141_F	0.510	0.21
99_T	154_L	0.510	0.21
5_G	9_K	0.510	0.21
178_T	189_L	0.509	0.21
111_G	168_N	0.509	0.21
294_E	308_V	0.508	0.21
160_M	180_A	0.508	0.21
6_L	101_G	0.508	0.21
178_T	280_I	0.508	0.21
117_V	307_A	0.507	0.21
141_F	243_I	0.507	0.21
65_F	177_F	0.505	0.21
73_G	163_G	0.504	0.21
59_D	309_I	0.504	0.21
153_M	241_T	0.504	0.21
83_I	89_F	0.504	0.21
204_F	247_I	0.504	0.21
161_A	279_I	0.502	0.21
152_S	200_G	0.502	0.21
101_G	105_H	0.502	0.21
4_S	85_R	0.501	0.21
24_V	29_N	0.501	0.21
164_A	252_F	0.500	0.20

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
2xq2A	2	0.2462	58.2	0.936	Contact Map
2nwlA	3	0.6954	37.6	0.943	Contact Map
2mfrA	1	0.1569	26.8	0.948	Contact Map
4av3A	2	0.2769	16.5	0.953	Contact Map
3dh4A	3	0.1877	13.4	0.954	Contact Map
2cfqA	1	0.7723	7.6	0.959	Contact Map
4c7rA	3	0.6985	5.3	0.962	Contact Map
4a01A	2	0.3015	3.8	0.964	Contact Map
3hd7A	1	0.1046	3.7	0.965	Contact Map
4o9uB	2	0.2585	3.4	0.965	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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