YVBG - BACSU - GREMLIN Contacts

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YVBG - UPF0056 membrane protein YvbG

UniProt:	O32244	Sequences: MMFSFIVHVFISLFAVSNPIGNVPIFLTLTEGYTAAERKAIARKAAILSFFILAAFLVFGHLIFKLFDINIHALRVAGGIFIFGIAYNLLNAKESHVQSLHHDEHKESKEKADISVTPLSIPIIAGPGTIATVMSLSAGHSGIGHYAAVMIGIAAVIALTFLFFHYSAFISSKLGKTEMNVITRLMGLILAVVAVGMIGAGLKGMFPVLTS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	211 (195)
Sequences:	2513 (1684)
Seq/√Len:	120.6

ECOLI - YCHE MARC YHGN
BACSU - YVBG
SULSO - Q7LXS5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
199_G	205_M	4.293	1.00
34_T	37_E	3.412	1.00
50_F	157_I	3.309	1.00
76_V	199_G	3.268	1.00
53_L	129_T	3.208	1.00
84_G	87_Y	3.004	1.00
73_A	196_G	2.921	1.00
161_F	165_H	2.771	1.00
43_R	161_F	2.619	1.00
72_H	204_G	2.555	1.00
10_F	155_A	2.544	1.00
48_L	116_V	2.401	1.00
196_G	200_A	2.365	1.00
52_I	121_I	2.354	1.00
50_F	154_A	2.217	1.00
6_I	152_G	2.141	1.00
175_G	178_E	2.125	1.00
61_H	65_K	2.096	1.00
9_V	152_G	2.046	1.00
83_F	198_I	2.045	1.00
46_A	157_I	2.006	1.00
47_I	51_F	1.987	1.00
26_F	30_T	1.966	1.00
6_I	151_I	1.928	1.00
10_F	159_L	1.915	1.00
54_A	150_M	1.877	1.00
58_V	150_M	1.838	1.00
49_S	157_I	1.815	1.00
86_A	191_A	1.805	1.00
39_K	165_H	1.781	1.00
72_H	75_R	1.750	1.00
50_F	54_A	1.732	1.00
17_S	156_V	1.709	1.00
88_N	93_K	1.687	1.00
80_I	83_F	1.669	1.00
203_K	206_F	1.668	1.00
18_N	21_G	1.648	1.00
48_L	120_S	1.648	1.00
169_F	172_S	1.636	1.00
76_V	205_M	1.593	1.00
13_L	133_V	1.529	1.00
53_L	125_A	1.529	1.00
75_R	200_A	1.514	1.00
137_S	146_Y	1.508	1.00
80_I	198_I	1.498	1.00
26_F	42_A	1.491	1.00
9_V	136_L	1.487	1.00
52_I	125_A	1.450	1.00
53_L	133_V	1.425	1.00
54_A	154_A	1.393	1.00
83_F	194_A	1.367	1.00
43_R	165_H	1.366	1.00
137_S	149_V	1.353	1.00
73_A	199_G	1.342	1.00
26_F	119_L	1.336	1.00
158_A	162_L	1.313	1.00
46_A	160_T	1.277	1.00
57_L	133_V	1.271	1.00
6_I	155_A	1.270	1.00
89_L	187_G	1.270	1.00
124_I	160_T	1.268	1.00
38_R	168_A	1.265	1.00
76_V	202_L	1.250	0.99
21_G	24_P	1.244	0.99
166_Y	169_F	1.243	0.99
33_Y	37_E	1.235	0.99
40_A	44_K	1.217	0.99
35_A	39_K	1.208	0.99
115_S	120_S	1.202	0.99
79_G	198_I	1.181	0.99
133_V	153_I	1.179	0.99
51_F	55_A	1.174	0.99
46_A	161_F	1.171	0.99
6_I	10_F	1.153	0.99
44_K	113_D	1.147	0.99
190_L	194_A	1.146	0.99
33_Y	41_I	1.141	0.99
75_R	204_G	1.135	0.99
17_S	157_I	1.132	0.99
79_G	201_G	1.131	0.99
89_L	186_M	1.131	0.99
57_L	150_M	1.126	0.99
70_N	196_G	1.125	0.99
59_F	63_I	1.122	0.99
169_F	173_K	1.104	0.99
45_A	49_S	1.104	0.99
22_N	164_F	1.102	0.99
81_F	191_A	1.101	0.99
35_A	38_R	1.099	0.99
13_L	153_I	1.096	0.99
15_A	18_N	1.092	0.99
57_L	137_S	1.084	0.98
199_G	202_L	1.079	0.98
30_T	38_R	1.076	0.98
144_G	147_A	1.073	0.98
15_A	67_F	1.070	0.98
80_I	87_Y	1.063	0.98
89_L	183_T	1.053	0.98
17_S	129_T	1.051	0.98
107_E	111_K	1.046	0.98
129_T	133_V	1.037	0.98
39_K	43_R	1.033	0.98
52_I	120_S	1.030	0.98
24_P	27_L	1.030	0.98
174_L	178_E	1.028	0.98
81_F	85_I	1.015	0.98
76_V	198_I	0.999	0.97
83_F	87_Y	0.990	0.97
16_V	128_G	0.986	0.97
83_F	191_A	0.984	0.97
43_R	47_I	0.981	0.97
16_V	132_T	0.970	0.97
191_A	194_A	0.969	0.97
64_F	192_V	0.969	0.97
162_L	166_Y	0.961	0.97
18_N	82_I	0.959	0.97
55_A	59_F	0.949	0.96
53_L	130_I	0.933	0.96
27_L	171_S	0.933	0.96
57_L	146_Y	0.931	0.96
76_V	201_G	0.930	0.96
147_A	151_I	0.916	0.96
94_E	97_V	0.906	0.95
146_Y	150_M	0.898	0.95
49_S	120_S	0.878	0.95
21_G	25_I	0.873	0.94
48_L	115_S	0.857	0.94
26_F	38_R	0.847	0.93
45_A	114_I	0.834	0.93
130_I	134_M	0.833	0.93
148_A	151_I	0.825	0.92
35_A	168_A	0.822	0.92
63_I	130_I	0.822	0.92
14_F	159_L	0.820	0.92
158_A	169_F	0.812	0.92
21_G	160_T	0.805	0.92
156_V	159_L	0.801	0.91
82_I	135_S	0.800	0.91
26_F	167_S	0.798	0.91
62_L	65_K	0.797	0.91
77_A	195_V	0.791	0.91
14_F	163_F	0.778	0.90
46_A	49_S	0.777	0.90
125_A	153_I	0.768	0.90
74_L	157_I	0.764	0.89
184_R	195_V	0.763	0.89
59_F	62_L	0.756	0.89
18_N	186_M	0.750	0.88
74_L	131_A	0.750	0.88
81_F	179_M	0.748	0.88
12_S	132_T	0.747	0.88
44_K	48_L	0.746	0.88
26_F	127_P	0.745	0.88
18_N	24_P	0.737	0.88
116_V	177_T	0.735	0.87
53_L	153_I	0.730	0.87
76_V	195_V	0.726	0.87
90_L	187_G	0.725	0.87
74_L	132_T	0.725	0.87
142_G	145_H	0.722	0.86
64_F	134_M	0.720	0.86
70_N	73_A	0.716	0.86
23_V	27_L	0.708	0.85
120_S	125_A	0.707	0.85
92_A	184_R	0.705	0.85
125_A	187_G	0.700	0.85
23_V	164_F	0.699	0.85
22_N	123_I	0.699	0.85
23_V	163_F	0.698	0.85
65_K	147_A	0.698	0.85
78_G	131_A	0.697	0.85
51_F	143_I	0.695	0.84
92_A	187_G	0.694	0.84
18_N	129_T	0.693	0.84
56_F	134_M	0.691	0.84
22_N	124_I	0.687	0.84
37_E	41_I	0.686	0.84
88_N	91_N	0.681	0.83
44_K	115_S	0.678	0.83
19_P	156_V	0.669	0.82
26_F	70_N	0.669	0.82
19_P	127_P	0.667	0.82
15_A	188_L	0.662	0.81
30_T	33_Y	0.661	0.81
18_N	56_F	0.659	0.81
73_A	77_A	0.657	0.81
177_T	181_V	0.651	0.80
152_G	156_V	0.651	0.80
22_N	81_F	0.648	0.80
13_L	53_L	0.647	0.80
86_A	90_L	0.642	0.79
202_L	206_F	0.634	0.79
113_D	202_L	0.634	0.79
5_F	140_H	0.633	0.78
39_K	161_F	0.633	0.78
67_F	135_S	0.630	0.78
86_A	180_N	0.629	0.78
81_F	133_V	0.629	0.78
40_A	202_L	0.629	0.78
42_A	182_I	0.628	0.78
95_S	98_Q	0.625	0.78
14_F	156_V	0.619	0.77
10_F	14_F	0.619	0.77
10_F	152_G	0.616	0.77
147_A	150_M	0.615	0.76
52_I	166_Y	0.613	0.76
88_N	97_V	0.610	0.76
64_F	78_G	0.608	0.76
78_G	89_L	0.607	0.75
12_S	16_V	0.602	0.75
86_A	194_A	0.601	0.75
185_L	189_I	0.595	0.74
136_L	149_V	0.594	0.74
72_H	199_G	0.592	0.74
15_A	191_A	0.591	0.74
81_F	123_I	0.591	0.74
108_S	111_K	0.590	0.73
186_M	197_M	0.589	0.73
74_L	188_L	0.588	0.73
155_A	173_K	0.586	0.73
121_I	188_L	0.586	0.73
66_L	193_V	0.585	0.73
128_G	184_R	0.579	0.72
82_I	193_V	0.579	0.72
18_N	77_A	0.578	0.72
117_T	190_L	0.577	0.72
57_L	185_L	0.575	0.71
182_I	206_F	0.575	0.71
41_I	45_A	0.574	0.71
141_S	148_A	0.572	0.71
12_S	188_L	0.570	0.71
123_I	126_G	0.570	0.71
14_F	88_N	0.568	0.71
109_K	206_F	0.566	0.70
176_K	180_N	0.564	0.70
20_I	182_I	0.563	0.70
73_A	205_M	0.561	0.70
92_A	186_M	0.560	0.70
15_A	72_H	0.555	0.69
69_I	95_S	0.551	0.68
16_V	193_V	0.550	0.68
89_L	116_V	0.549	0.68
129_T	153_I	0.547	0.68
148_A	152_G	0.547	0.68
57_L	153_I	0.546	0.68
13_L	17_S	0.545	0.67
8_H	11_I	0.544	0.67
93_K	96_H	0.543	0.67
84_G	91_N	0.542	0.67
128_G	190_L	0.539	0.67
122_P	126_G	0.539	0.67
114_I	119_L	0.537	0.66
12_S	68_D	0.537	0.66
67_F	194_A	0.536	0.66
56_F	124_I	0.535	0.66
37_E	40_A	0.534	0.66
49_S	124_I	0.532	0.66
27_L	182_I	0.532	0.66
13_L	174_L	0.531	0.65
131_A	134_M	0.529	0.65
45_A	120_S	0.529	0.65
64_F	70_N	0.528	0.65
92_A	180_N	0.528	0.65
156_V	160_T	0.526	0.65
36_A	39_K	0.524	0.64
151_I	172_S	0.522	0.64
16_V	52_I	0.521	0.64
27_L	119_L	0.521	0.64
15_A	192_V	0.520	0.64
125_A	189_I	0.519	0.64
179_M	188_L	0.518	0.64
92_A	181_V	0.518	0.64
71_I	86_A	0.518	0.64
24_P	124_I	0.517	0.63
65_K	172_S	0.515	0.63
36_A	173_K	0.514	0.63
181_V	185_L	0.514	0.63
90_L	194_A	0.512	0.63
59_F	135_S	0.509	0.62
152_G	155_A	0.508	0.62
83_F	195_V	0.508	0.62
74_L	206_F	0.507	0.62
60_G	126_G	0.507	0.62
48_L	56_F	0.506	0.62
20_I	64_F	0.505	0.62
128_G	175_G	0.504	0.61
15_A	183_T	0.504	0.61
118_P	175_G	0.503	0.61
64_F	74_L	0.503	0.61
24_P	123_I	0.502	0.61
5_F	148_A	0.501	0.61
29_L	114_I	0.500	0.61

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
4j05A	3	0.5118	14.2	0.95	Contact Map
2cfqA	1	0.5024	13.6	0.951	Contact Map
4w6vA	1	0.455	12.9	0.951	Contact Map
1pw4A	1	0.5024	11.5	0.952	Contact Map
4kjrA	3	0.3744	7	0.957	Contact Map
4dx5A	3	0.9384	7	0.957	Contact Map
4wgvA	2	0.3886	6.7	0.957	Contact Map
4cz8A	2	0.7725	6.6	0.957	Contact Map
3w9iA	3	0.9336	5.6	0.959	Contact Map
4xnjA	1	0.9384	5.6	0.959	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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