YICG - ECOLI - GREMLIN Contacts

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YICG - UPF0126 inner membrane protein YicG

UniProt:	P0AGM2	Sequences: MLLHILYLVGITAEAMTGALAAGRRRMDTFGVIIIATATAIGGGSVRDILLGHYPLGWVKHPEYVIIVATAAVLTTIVAPVMPYLRKVFLVLDALGLVVFSIIGAQVALDMGHGPIIAVVAAVTTGVFGGVLRDMFCKRIPLVFQKELYAGVSFASAVLYIALQHYVSNHDVVIISTLVFGFFARLLALRLKLGLPVFYYSHEGH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11683
Length:	205 (195)
Sequences:	2535 (1767)
Seq/√Len:	126.5

ECOLI - YICG YADS
BACSU - YVGT
HALSA - Q9HSC6
SULSO - Q981D4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
101_S	153_S	3.992	1.00
25_R	139_R	3.787	1.00
35_I	137_C	3.470	1.00
36_A	72_A	3.315	1.00
12_T	71_A	3.247	1.00
159_L	180_F	3.176	1.00
187_L	191_L	3.071	1.00
156_S	181_G	3.026	1.00
38_A	136_F	2.792	1.00
98_V	182_F	2.691	1.00
45_S	58_W	2.645	1.00
95_L	182_F	2.564	1.00
182_F	186_L	2.495	1.00
105_A	157_A	2.460	1.00
109_L	118_A	2.403	1.00
97_L	126_G	2.310	1.00
27_M	137_C	2.192	1.00
90_L	189_L	2.137	1.00
91_V	186_L	2.089	1.00
187_L	193_L	2.054	1.00
123_V	154_F	2.030	1.00
21_A	137_C	1.978	1.00
148_L	152_V	1.962	1.00
175_I	179_V	1.917	1.00
97_L	153_S	1.833	1.00
4_H	8_L	1.754	1.00
162_A	166_Y	1.661	1.00
51_L	113_H	1.656	1.00
41_I	68_V	1.654	1.00
139_R	145_Q	1.611	1.00
40_A	68_V	1.609	1.00
14_E	96_G	1.600	1.00
163_L	168_S	1.593	1.00
52_G	55_P	1.563	1.00
108_A	121_A	1.558	1.00
119_V	161_I	1.534	1.00
62_P	66_I	1.534	1.00
155_A	184_A	1.518	1.00
152_V	184_A	1.507	1.00
105_A	118_A	1.487	1.00
16_M	75_T	1.472	1.00
118_A	161_I	1.470	1.00
105_A	161_I	1.468	1.00
37_T	68_V	1.461	1.00
113_H	117_I	1.442	1.00
7_Y	64_Y	1.417	1.00
136_F	144_F	1.415	1.00
10_G	14_E	1.405	1.00
188_A	193_L	1.398	1.00
107_V	111_M	1.392	1.00
127_V	143_V	1.381	1.00
26_R	197_V	1.381	1.00
119_V	158_V	1.369	1.00
50_L	59_V	1.365	1.00
46_V	124_T	1.330	1.00
33_I	69_A	1.328	1.00
163_L	173_V	1.327	1.00
4_H	61_H	1.316	1.00
66_I	70_T	1.308	1.00
29_T	76_T	1.301	1.00
179_V	183_F	1.299	1.00
51_L	111_M	1.290	1.00
174_I	178_L	1.277	1.00
46_V	128_F	1.273	1.00
30_F	150_A	1.270	1.00
121_A	125_T	1.269	1.00
146_K	194_G	1.252	1.00
42_G	132_L	1.244	1.00
38_A	132_L	1.228	0.99
98_V	102_I	1.218	0.99
173_V	177_T	1.209	0.99
98_V	178_L	1.189	0.99
131_V	143_V	1.182	0.99
101_S	105_A	1.176	0.99
71_A	75_T	1.174	0.99
36_A	68_V	1.174	0.99
94_A	186_L	1.173	0.99
4_H	63_E	1.171	0.99
115_P	161_I	1.160	0.99
12_T	67_I	1.156	0.99
101_S	181_G	1.131	0.99
94_A	182_F	1.116	0.99
69_A	73_V	1.107	0.99
102_I	181_G	1.096	0.99
33_I	72_A	1.096	0.99
32_V	76_T	1.080	0.99
98_V	156_S	1.077	0.99
54_Y	107_V	1.076	0.99
101_S	157_A	1.057	0.98
19_A	32_V	1.050	0.98
34_I	150_A	1.038	0.98
90_L	94_A	1.026	0.98
155_A	180_F	1.026	0.98
169_N	172_V	1.025	0.98
158_V	162_A	1.025	0.98
45_S	128_F	1.021	0.98
23_G	32_V	0.999	0.98
151_G	195_L	0.998	0.98
105_A	122_A	0.994	0.98
184_A	193_L	0.994	0.98
11_I	14_E	0.990	0.98
152_V	156_S	0.987	0.98
115_P	119_V	0.986	0.98
162_A	165_H	0.969	0.97
105_A	160_Y	0.967	0.97
186_L	190_R	0.959	0.97
6_L	99_V	0.956	0.97
58_W	117_I	0.951	0.97
34_I	144_F	0.947	0.97
11_I	41_I	0.942	0.97
102_I	177_T	0.939	0.97
96_G	100_F	0.936	0.97
188_A	192_K	0.931	0.97
16_M	92_L	0.929	0.97
11_I	15_A	0.928	0.96
156_S	177_T	0.925	0.96
180_F	184_A	0.921	0.96
99_V	178_L	0.920	0.96
58_W	128_F	0.920	0.96
141_P	144_F	0.917	0.96
17_T	92_L	0.901	0.96
122_A	177_T	0.893	0.96
68_V	76_T	0.892	0.96
54_Y	111_M	0.890	0.96
46_V	132_L	0.890	0.96
14_E	17_T	0.881	0.95
106_Q	110_D	0.881	0.95
13_A	96_G	0.878	0.95
160_Y	177_T	0.874	0.95
99_V	103_I	0.871	0.95
10_G	100_F	0.863	0.95
159_L	163_L	0.862	0.95
98_V	181_G	0.845	0.94
30_F	127_V	0.845	0.94
194_G	197_V	0.840	0.94
27_M	140_I	0.837	0.94
45_S	57_G	0.830	0.94
126_G	181_G	0.826	0.93
123_V	127_V	0.825	0.93
89_F	92_L	0.821	0.93
12_T	16_M	0.816	0.93
148_L	184_A	0.814	0.93
37_T	65_V	0.812	0.93
74_L	162_A	0.809	0.93
16_M	71_A	0.801	0.92
22_A	32_V	0.784	0.92
95_L	99_V	0.781	0.91
117_I	121_A	0.779	0.91
51_L	108_A	0.769	0.91
23_G	79_A	0.761	0.90
102_I	163_L	0.761	0.90
70_T	74_L	0.758	0.90
118_A	122_A	0.750	0.90
119_V	154_F	0.749	0.90
8_L	67_I	0.732	0.88
28_D	141_P	0.725	0.88
30_F	34_I	0.724	0.88
148_L	195_L	0.723	0.88
6_L	178_L	0.723	0.88
123_V	150_A	0.723	0.88
164_Q	173_V	0.722	0.88
168_S	172_V	0.712	0.87
30_F	154_F	0.710	0.87
159_L	177_T	0.708	0.87
131_V	136_F	0.698	0.86
51_L	54_Y	0.697	0.86
56_L	59_V	0.696	0.86
62_P	114_G	0.696	0.86
76_T	198_F	0.696	0.86
140_I	143_V	0.688	0.85
106_Q	160_Y	0.685	0.85
19_A	75_T	0.684	0.85
68_V	72_A	0.681	0.85
7_Y	14_E	0.681	0.85
7_Y	21_A	0.680	0.85
113_H	118_A	0.677	0.84
45_S	50_L	0.675	0.84
37_T	72_A	0.673	0.84
69_A	72_A	0.673	0.84
25_R	105_A	0.671	0.84
41_I	65_V	0.669	0.84
50_L	124_T	0.668	0.83
114_G	121_A	0.667	0.83
155_A	186_L	0.666	0.83
9_V	193_L	0.666	0.83
105_A	181_G	0.665	0.83
35_I	132_L	0.665	0.83
85_L	88_V	0.665	0.83
14_E	18_G	0.664	0.83
186_L	189_L	0.660	0.83
161_I	164_Q	0.655	0.82
131_V	144_F	0.651	0.82
57_G	64_Y	0.648	0.82
65_V	116_I	0.646	0.81
8_L	12_T	0.645	0.81
131_V	142_L	0.640	0.81
37_T	41_I	0.639	0.81
103_I	125_T	0.636	0.80
21_A	25_R	0.634	0.80
72_A	76_T	0.630	0.80
7_Y	16_M	0.629	0.80
68_V	71_A	0.627	0.79
160_Y	164_Q	0.627	0.79
100_F	126_G	0.626	0.79
103_I	177_T	0.620	0.79
51_L	107_V	0.620	0.79
163_L	177_T	0.620	0.79
140_I	145_Q	0.619	0.79
98_V	122_A	0.617	0.78
172_V	176_S	0.614	0.78
58_W	160_Y	0.613	0.78
19_A	72_A	0.608	0.77
9_V	13_A	0.605	0.77
154_F	157_A	0.603	0.77
131_V	172_V	0.602	0.77
91_V	95_L	0.599	0.76
46_V	50_L	0.599	0.76
66_I	116_I	0.598	0.76
159_L	176_S	0.596	0.76
97_L	181_G	0.593	0.76
18_G	143_V	0.590	0.75
3_L	99_V	0.590	0.75
152_V	188_A	0.590	0.75
31_G	35_I	0.589	0.75
59_V	117_I	0.587	0.75
35_I	138_K	0.586	0.75
65_V	120_V	0.585	0.75
39_T	42_G	0.584	0.74
19_A	23_G	0.583	0.74
27_M	144_F	0.582	0.74
102_I	160_Y	0.580	0.74
23_G	198_F	0.578	0.74
37_T	40_A	0.578	0.74
7_Y	11_I	0.567	0.72
32_V	72_A	0.567	0.72
7_Y	120_V	0.566	0.72
127_V	150_A	0.565	0.72
41_I	152_V	0.563	0.72
5_I	9_V	0.561	0.72
17_T	96_G	0.560	0.71
9_V	37_T	0.557	0.71
56_L	77_I	0.556	0.71
69_A	116_I	0.553	0.70
24_R	27_M	0.548	0.70
28_D	149_Y	0.546	0.70
38_A	42_G	0.545	0.69
165_H	179_V	0.544	0.69
34_I	120_V	0.543	0.69
164_Q	170_H	0.541	0.69
57_G	125_T	0.541	0.69
15_A	71_A	0.540	0.69
112_G	115_P	0.538	0.68
138_K	187_L	0.538	0.68
35_I	125_T	0.536	0.68
12_T	36_A	0.534	0.68
98_V	118_A	0.533	0.68
99_V	107_V	0.531	0.67
109_L	164_Q	0.529	0.67
29_T	190_R	0.529	0.67
172_V	175_I	0.527	0.67
183_F	187_L	0.525	0.67
101_S	156_S	0.525	0.67
52_G	56_L	0.524	0.66
114_G	117_I	0.523	0.66
18_G	154_F	0.523	0.66
146_K	188_A	0.522	0.66
27_M	31_G	0.522	0.66
34_I	128_F	0.520	0.66
122_A	152_V	0.520	0.66
13_A	92_L	0.519	0.66
7_Y	89_F	0.518	0.65
48_D	107_V	0.517	0.65
10_G	92_L	0.516	0.65
13_A	67_I	0.516	0.65
57_G	121_A	0.515	0.65
3_L	172_V	0.515	0.65
173_V	181_G	0.515	0.65
24_R	139_R	0.514	0.65
8_L	155_A	0.510	0.64
62_P	126_G	0.509	0.64
23_G	75_T	0.508	0.64
19_A	36_A	0.508	0.64
168_S	173_V	0.507	0.64
45_S	49_I	0.507	0.64
98_V	189_L	0.507	0.64
135_M	180_F	0.506	0.64
29_T	146_K	0.506	0.64
147_E	192_K	0.504	0.63
26_R	124_T	0.504	0.63
59_V	114_G	0.501	0.63
103_I	107_V	0.501	0.63
70_T	77_I	0.500	0.63

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
2f2bA	4	0.4098	6.6	0.962	Contact Map
3llqA	3	0.4049	6	0.963	Contact Map
3gd8A	4	0.4146	3.3	0.967	Contact Map
2o9gA	3	0.4049	2.6	0.969	Contact Map
1s4zC	1	0.1415	1.6	0.972	Contact Map
3cn5A	3	0.4195	1.4	0.973	Contact Map
3wdoA	1	0.8537	1.2	0.974	Contact Map
3i71A	3	0.2	1.2	0.974	Contact Map
4qncA	2	0.361	1.1	0.975	Contact Map
4b19A	1	0.1463	1.1	0.975	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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