YTRC - BACSU - GREMLIN Contacts

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YTRC - Probable ABC transporter permease YtrC

UniProt:	O34898	Sequences: MVDRGLLYREWKQNQVVILLSIAFLVLANPLSIVNTYLSYQGCLDRQDPQYCDFIVNYSISNLIDINWVPGVILAVCFLGMERSKGTMDFILSLPYNRSQIFQTKFWLGGFVIVLSQLIGFLLAWLLILVYNPEHVYFFEHSSIGVIVISFMAFSLVMAAGALTGNAFAQLLTAFSAAILPYLIIALPVGNLEVVFGANIWEIFPSPESYFSLASNLSNLVPISYVVNEWLINSKYLLLIPAVMSMLFYLIGFISFKKLPSERNGHFFLWNRLDRPVQILVMAFGILGFGLFGYYTGHSIIGYILGMIIGAVAGFFVSYFSIYKKTKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	328 (312)
Sequences:	572 (475)
Seq/√Len:	26.9

BACSU - YTRC YTRD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
102_F	252_G	6.322	1.00
10_E	105_K	3.892	1.00
114_V	147_I	3.869	1.00
109_G	154_F	3.708	1.00
106_F	155_S	3.625	1.00
82_E	259_L	3.362	1.00
306_G	310_G	3.329	1.00
244_M	248_F	3.228	1.00
278_Q	319_Y	3.111	1.00
26_V	120_G	3.091	1.00
161_G	170_Q	3.077	1.00
219_N	222_P	3.061	1.00
286_I	289_F	2.937	1.00
78_F	154_F	2.812	1.00
103_Q	249_Y	2.791	1.00
277_V	283_A	2.747	1.00
83_R	161_G	2.737	1.00
88_M	261_S	2.595	0.99
154_F	164_T	2.456	0.99
99_S	253_F	2.412	0.99
92_L	256_F	2.390	0.99
148_V	245_S	2.368	0.99
183_L	283_A	2.323	0.98
301_I	305_L	2.259	0.98
119_I	122_L	2.247	0.98
99_S	257_K	2.228	0.98
98_R	101_I	2.192	0.98
289_F	306_G	2.187	0.98
92_L	261_S	2.170	0.97
97_N	257_K	2.155	0.97
110_G	114_V	2.102	0.97
176_S	283_A	2.082	0.97
176_S	277_V	1.992	0.96
92_L	101_I	1.987	0.96
81_M	116_S	1.980	0.96
165_G	265_G	1.885	0.94
102_F	164_T	1.824	0.93
284_F	288_G	1.801	0.93
79_L	158_M	1.799	0.93
82_E	105_K	1.772	0.92
75_A	289_F	1.767	0.92
180_L	283_A	1.739	0.91
83_R	170_Q	1.730	0.91
222_P	225_Y	1.723	0.91
81_M	259_L	1.686	0.90
80_G	170_Q	1.668	0.90
82_E	264_N	1.659	0.89
183_L	187_L	1.648	0.89
216_N	222_P	1.644	0.89
259_L	264_N	1.613	0.88
156_L	184_I	1.601	0.88
89_D	93_S	1.598	0.87
283_A	322_I	1.578	0.87
9_R	82_E	1.576	0.87
169_A	195_V	1.574	0.87
7_L	108_L	1.574	0.87
259_L	319_Y	1.568	0.86
21_S	25_L	1.557	0.86
175_F	314_G	1.547	0.86
251_I	258_K	1.501	0.84
92_L	319_Y	1.484	0.83
89_D	267_F	1.484	0.83
94_L	101_I	1.483	0.83
12_K	15_Q	1.460	0.82
68_W	276_P	1.458	0.82
106_F	154_F	1.408	0.80
218_S	222_P	1.396	0.79
160_A	164_T	1.395	0.79
165_G	262_E	1.387	0.79
299_S	304_I	1.361	0.77
90_F	196_F	1.356	0.77
163_L	173_T	1.355	0.77
82_E	108_L	1.352	0.77
110_G	151_F	1.346	0.76
155_S	245_S	1.344	0.76
318_S	322_I	1.335	0.76
221_V	224_S	1.326	0.75
74_L	113_I	1.323	0.75
285_G	311_A	1.316	0.75
9_R	264_N	1.311	0.75
169_A	265_G	1.300	0.74
280_L	284_F	1.298	0.74
180_L	184_I	1.292	0.73
145_G	238_L	1.292	0.73
14_N	78_F	1.286	0.73
22_I	119_I	1.283	0.73
111_F	119_I	1.280	0.73
27_L	305_L	1.271	0.72
113_I	150_S	1.267	0.72
9_R	13_Q	1.240	0.70
169_A	267_F	1.236	0.70
91_I	259_L	1.233	0.70
82_E	161_G	1.233	0.70
159_A	248_F	1.232	0.70
310_G	314_G	1.227	0.69
172_L	176_S	1.226	0.69
11_W	19_L	1.223	0.69
163_L	255_S	1.216	0.69
133_P	137_Y	1.205	0.68
82_E	91_I	1.205	0.68
317_V	321_S	1.188	0.67
74_L	102_F	1.186	0.67
48_D	144_I	1.181	0.66
81_M	92_L	1.178	0.66
87_T	91_I	1.177	0.66
92_L	116_S	1.173	0.66
79_L	161_G	1.172	0.66
9_R	91_I	1.170	0.66
81_M	91_I	1.163	0.65
101_I	105_K	1.157	0.65
101_I	256_F	1.156	0.65
174_A	181_P	1.143	0.64
121_F	143_S	1.143	0.64
302_G	306_G	1.138	0.64
281_V	306_G	1.134	0.63
88_M	92_L	1.131	0.63
82_E	267_F	1.119	0.62
52_C	249_Y	1.117	0.62
134_E	137_Y	1.116	0.62
5_G	14_N	1.114	0.62
283_A	286_I	1.113	0.62
6_L	91_I	1.092	0.60
188_P	192_L	1.090	0.60
83_R	264_N	1.087	0.60
27_L	31_L	1.081	0.59
320_F	324_K	1.080	0.59
47_Q	73_I	1.071	0.59
123_L	185_I	1.067	0.58
314_G	318_S	1.064	0.58
221_V	271_N	1.062	0.58
30_P	314_G	1.062	0.58
26_V	313_A	1.058	0.58
82_E	87_T	1.057	0.58
80_G	106_F	1.055	0.58
19_L	73_I	1.055	0.58
38_L	168_F	1.048	0.57
23_A	61_S	1.046	0.57
89_D	259_L	1.042	0.57
170_Q	306_G	1.041	0.57
15_Q	89_D	1.034	0.56
66_I	151_F	1.033	0.56
42_G	168_F	1.033	0.56
105_K	108_L	1.032	0.56
264_N	319_Y	1.023	0.55
305_L	309_I	1.021	0.55
246_M	304_I	1.017	0.55
159_A	255_S	1.009	0.54
163_L	274_D	1.009	0.54
214_A	217_L	1.006	0.54
180_L	277_V	1.006	0.54
263_R	274_D	1.004	0.54
8_Y	11_W	0.999	0.53
78_F	181_P	0.994	0.53
193_E	282_M	0.989	0.53
80_G	167_A	0.986	0.52
144_I	246_M	0.986	0.52
16_V	178_A	0.980	0.52
280_L	314_G	0.975	0.52
85_K	89_D	0.973	0.51
13_Q	89_D	0.970	0.51
284_F	287_L	0.969	0.51
72_V	308_I	0.967	0.51
216_N	219_N	0.967	0.51
9_R	14_N	0.966	0.51
222_P	229_E	0.960	0.50
41_Q	73_I	0.955	0.50
24_F	114_V	0.955	0.50
6_L	83_R	0.945	0.49
191_N	195_V	0.944	0.49
24_F	100_Q	0.943	0.49
176_S	179_I	0.937	0.49
6_L	101_I	0.936	0.49
150_S	163_L	0.931	0.48
198_A	320_F	0.926	0.48
117_Q	143_S	0.925	0.48
187_L	315_F	0.925	0.48
159_A	256_F	0.924	0.48
176_S	273_L	0.923	0.48
38_L	53_D	0.914	0.47
126_L	132_N	0.914	0.47
97_N	253_F	0.913	0.47
277_V	281_V	0.913	0.47
20_L	139_F	0.909	0.47
215_S	218_S	0.907	0.46
97_N	152_M	0.904	0.46
142_S	198_A	0.904	0.46
11_W	279_I	0.904	0.46
37_Y	131_Y	0.902	0.46
214_A	221_V	0.899	0.46
75_A	157_V	0.891	0.45
23_A	260_P	0.889	0.45
94_L	259_L	0.887	0.45
144_I	148_V	0.886	0.45
34_V	252_G	0.886	0.45
92_L	259_L	0.884	0.45
33_I	124_A	0.882	0.45
76_V	227_V	0.881	0.45
179_I	313_A	0.880	0.44
90_F	108_L	0.877	0.44
144_I	251_I	0.876	0.44
141_H	250_L	0.876	0.44
199_N	279_I	0.870	0.44
259_L	267_F	0.865	0.43
114_V	136_V	0.863	0.43
79_L	162_A	0.860	0.43
80_G	83_R	0.855	0.43
198_A	315_F	0.855	0.43
6_L	155_S	0.853	0.42
75_A	153_A	0.852	0.42
246_M	257_K	0.851	0.42
263_R	266_H	0.851	0.42
8_Y	29_N	0.849	0.42
83_R	259_L	0.849	0.42
284_F	314_G	0.843	0.42
313_A	321_S	0.842	0.42
289_F	303_Y	0.838	0.41
42_G	247_L	0.836	0.41
105_K	285_G	0.832	0.41
239_L	312_V	0.828	0.41
259_L	269_L	0.828	0.41
69_V	221_V	0.826	0.41
78_F	113_I	0.824	0.40
157_V	174_A	0.824	0.40
287_L	293_G	0.824	0.40
281_V	285_G	0.824	0.40
257_K	261_S	0.823	0.40
6_L	105_K	0.820	0.40
187_L	288_G	0.819	0.40
172_L	280_L	0.817	0.40
144_I	301_I	0.817	0.40
147_I	242_A	0.812	0.40
225_Y	228_N	0.810	0.39
109_G	256_F	0.806	0.39
79_L	83_R	0.805	0.39
15_Q	18_I	0.805	0.39
163_L	273_L	0.805	0.39
180_L	324_K	0.802	0.39
95_P	116_S	0.801	0.39
163_L	169_A	0.800	0.39
16_V	109_G	0.798	0.39
39_S	246_M	0.796	0.38
9_R	89_D	0.795	0.38
243_V	250_L	0.794	0.38
98_R	256_F	0.789	0.38
268_F	274_D	0.788	0.38
78_F	86_G	0.787	0.38
40_Y	85_K	0.786	0.38
183_L	288_G	0.783	0.37
58_Y	65_D	0.780	0.37
46_R	49_P	0.775	0.37
71_G	75_A	0.774	0.37
23_A	111_F	0.769	0.36
23_A	287_L	0.767	0.36
271_N	300_I	0.766	0.36
260_P	263_R	0.766	0.36
12_K	271_N	0.765	0.36
4_R	83_R	0.761	0.36
286_I	315_F	0.757	0.36
105_K	264_N	0.757	0.36
96_Y	238_L	0.751	0.35
288_G	306_G	0.745	0.35
6_L	96_Y	0.742	0.35
7_L	11_W	0.741	0.35
102_F	226_V	0.739	0.34
322_I	325_K	0.738	0.34
83_R	281_V	0.738	0.34
198_A	241_P	0.735	0.34
150_S	325_K	0.733	0.34
242_A	311_A	0.732	0.34
122_L	246_M	0.729	0.34
10_E	108_L	0.726	0.34
244_M	295_Y	0.726	0.34
94_L	277_V	0.725	0.33
159_A	259_L	0.723	0.33
198_A	324_K	0.722	0.33
176_S	284_F	0.722	0.33
24_F	254_I	0.721	0.33
71_G	98_R	0.718	0.33
91_I	105_K	0.718	0.33
13_Q	177_A	0.717	0.33
21_S	82_E	0.713	0.33
52_C	126_L	0.708	0.32
285_G	291_L	0.708	0.32
68_W	249_Y	0.707	0.32
140_E	313_A	0.700	0.32
26_V	188_P	0.699	0.32
82_E	96_Y	0.699	0.32
319_Y	323_Y	0.697	0.32
153_A	184_I	0.696	0.32
25_L	117_Q	0.695	0.31
239_L	246_M	0.694	0.31
101_I	325_K	0.694	0.31
242_A	291_L	0.693	0.31
111_F	242_A	0.690	0.31
15_Q	178_A	0.689	0.31
85_K	169_A	0.689	0.31
243_V	247_L	0.688	0.31
44_L	152_M	0.686	0.31
160_A	177_A	0.686	0.31
81_M	270_W	0.686	0.31
238_L	287_L	0.685	0.31
221_V	227_V	0.684	0.31
82_E	319_Y	0.680	0.31
238_L	242_A	0.680	0.31
73_I	182_Y	0.680	0.31
92_L	95_P	0.679	0.30
151_F	312_V	0.678	0.30
268_F	273_L	0.676	0.30
80_G	84_S	0.674	0.30
9_R	267_F	0.673	0.30
69_V	177_A	0.673	0.30
244_M	311_A	0.672	0.30
292_F	306_G	0.670	0.30
21_S	30_P	0.664	0.29
33_I	285_G	0.664	0.29
9_R	83_R	0.663	0.29
83_R	96_Y	0.661	0.29
39_S	47_Q	0.659	0.29
89_D	266_H	0.657	0.29
83_R	105_K	0.655	0.29
66_I	168_F	0.654	0.29
163_L	177_A	0.651	0.29
26_V	296_T	0.650	0.29
9_R	87_T	0.647	0.28
320_F	325_K	0.646	0.28
114_V	221_V	0.644	0.28
148_V	238_L	0.643	0.28
24_F	29_N	0.639	0.28
94_L	228_N	0.638	0.28
116_S	198_A	0.637	0.28
272_R	317_V	0.634	0.28
121_F	142_S	0.633	0.28
96_Y	309_I	0.632	0.28
87_T	180_L	0.632	0.28
242_A	254_I	0.630	0.27
184_I	313_A	0.627	0.27
43_C	126_L	0.627	0.27
45_D	48_D	0.626	0.27
164_T	173_T	0.626	0.27
78_F	109_G	0.624	0.27
199_N	305_L	0.623	0.27
52_C	127_L	0.622	0.27
283_A	287_L	0.621	0.27
120_G	123_L	0.618	0.27
123_L	151_F	0.617	0.27
223_I	243_V	0.616	0.27
151_F	229_E	0.615	0.27
145_G	317_V	0.614	0.26
142_S	154_F	0.613	0.26
107_W	115_L	0.613	0.26
274_D	322_I	0.612	0.26
170_Q	281_V	0.612	0.26
54_F	132_N	0.611	0.26
64_I	218_S	0.610	0.26
65_D	111_F	0.606	0.26
62_N	73_I	0.604	0.26
111_F	235_K	0.604	0.26
285_G	292_F	0.603	0.26
132_N	149_I	0.601	0.26
234_S	324_K	0.601	0.26
92_L	142_S	0.599	0.26
50_Q	62_N	0.597	0.25
37_Y	282_M	0.597	0.25
177_A	183_L	0.594	0.25
275_R	278_Q	0.593	0.25
46_R	111_F	0.592	0.25
268_F	277_V	0.591	0.25
79_L	102_F	0.591	0.25
72_V	109_G	0.590	0.25
95_P	268_F	0.590	0.25
80_G	181_P	0.588	0.25
315_F	324_K	0.588	0.25
182_Y	246_M	0.587	0.25
83_R	92_L	0.587	0.25
173_T	277_V	0.585	0.25
114_V	175_F	0.585	0.25
264_N	269_L	0.581	0.25
30_P	109_G	0.581	0.25
40_Y	97_N	0.580	0.25
216_N	251_I	0.578	0.24
114_V	153_A	0.577	0.24
34_V	219_N	0.575	0.24
16_V	169_A	0.574	0.24
17_V	163_L	0.574	0.24
191_N	251_I	0.572	0.24
49_P	119_I	0.572	0.24
130_V	184_I	0.571	0.24
175_F	277_V	0.571	0.24
219_N	225_Y	0.570	0.24
79_L	259_L	0.566	0.24
142_S	261_S	0.566	0.24
254_I	308_I	0.565	0.24
241_P	277_V	0.564	0.24
288_G	310_G	0.563	0.24
142_S	277_V	0.562	0.24
98_R	155_S	0.561	0.23
235_K	247_L	0.561	0.23
54_F	151_F	0.558	0.23
158_M	178_A	0.558	0.23
64_I	70_P	0.558	0.23
164_T	264_N	0.557	0.23
117_Q	160_A	0.555	0.23
10_E	101_I	0.555	0.23
149_I	307_M	0.554	0.23
48_D	247_L	0.553	0.23
50_Q	53_D	0.552	0.23
99_S	103_Q	0.551	0.23
88_M	259_L	0.551	0.23
92_L	264_N	0.549	0.23
33_I	280_L	0.548	0.23
11_W	114_V	0.548	0.23
68_W	77_C	0.545	0.23
281_V	286_I	0.544	0.23
145_G	157_V	0.543	0.23
11_W	82_E	0.543	0.23
125_W	246_M	0.542	0.22
285_G	322_I	0.542	0.22
116_S	119_I	0.541	0.22
13_Q	181_P	0.540	0.22
173_T	315_F	0.540	0.22
159_A	176_S	0.539	0.22
102_F	106_F	0.539	0.22
64_I	190_G	0.539	0.22
195_V	315_F	0.538	0.22
71_G	160_A	0.537	0.22
71_G	150_S	0.535	0.22
187_L	289_F	0.534	0.22
152_M	191_N	0.532	0.22
8_Y	257_K	0.532	0.22
78_F	105_K	0.532	0.22
71_G	259_L	0.532	0.22
79_L	82_E	0.531	0.22
73_I	111_F	0.531	0.22
98_R	277_V	0.531	0.22
80_G	285_G	0.530	0.22
70_P	153_A	0.528	0.22
95_P	269_L	0.528	0.22
169_A	264_N	0.526	0.22
132_N	137_Y	0.526	0.22
23_A	145_G	0.525	0.22
298_H	311_A	0.524	0.22
73_I	191_N	0.522	0.21
221_V	226_V	0.521	0.21
188_P	224_S	0.521	0.21
289_F	307_M	0.520	0.21
177_A	275_R	0.519	0.21
129_L	242_A	0.519	0.21
71_G	78_F	0.518	0.21
130_V	151_F	0.517	0.21
84_S	87_T	0.516	0.21
57_N	184_I	0.515	0.21
90_F	123_L	0.513	0.21
193_E	300_I	0.513	0.21
151_F	245_S	0.512	0.21
97_N	111_F	0.511	0.21
27_L	67_N	0.510	0.21
160_A	320_F	0.508	0.21
27_L	309_I	0.508	0.21
9_R	104_T	0.508	0.21
97_N	272_R	0.507	0.21
26_V	256_F	0.507	0.21
195_V	304_I	0.506	0.21
8_Y	102_F	0.505	0.21
262_E	265_G	0.505	0.21
22_I	193_E	0.504	0.21
75_A	95_P	0.501	0.20
239_L	257_K	0.500	0.20
82_E	92_L	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	0.2348	49.5	0.94	Contact Map
4av3A	2	0.2713	12.7	0.956	Contact Map
2mfrA	1	0.1555	12	0.956	Contact Map
4hw9A	3	0.2683	8.1	0.959	Contact Map
3dh4A	3	0.1768	8.1	0.959	Contact Map
3hd7A	1	0.1037	7.9	0.959	Contact Map
1iijA	1	0.1067	6.8	0.961	Contact Map
2kv5A	1	0.1006	5.7	0.962	Contact Map
5ajiA	3	0.2957	5.2	0.963	Contact Map
1v54A	1	0.3201	5.2	0.963	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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