YWDK - BACSU - GREMLIN Contacts

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YWDK - UPF0382 membrane protein YwdK

UniProt:	P39619	Sequences: MKVFIILGAINALLAVGLGAFGAHGLEGKIPDKYLQVWHTGVQYHMYHALGLFVVAFLADKLSGIGSVTTAGWLMFAGIVLFSGSLYILSVTQISILGAITPLGGVAFIISWIMIVVAAVKYL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	123 (116)
Sequences:	1567 (1151)
Seq/√Len:	106.9

ECOLI - YGDD
BACSU - YWDK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_L	109_I	4.594	1.00
39_H	43_Q	3.117	1.00
75_M	111_S	2.477	1.00
4_F	72_G	2.466	1.00
17_G	109_I	2.410	1.00
11_N	49_A	2.396	1.00
12_A	51_G	2.169	1.00
12_A	49_A	2.096	1.00
51_G	75_M	2.095	1.00
22_G	38_W	2.016	1.00
13_L	113_I	2.004	1.00
30_I	90_S	1.980	1.00
74_L	107_A	1.950	1.00
6_I	116_V	1.919	1.00
8_G	53_F	1.866	1.00
27_E	33_K	1.796	1.00
37_V	86_L	1.757	1.00
96_I	99_A	1.737	1.00
67_S	114_M	1.737	1.00
45_H	87_Y	1.732	1.00
74_L	110_I	1.659	1.00
79_I	108_F	1.631	1.00
85_S	101_T	1.630	1.00
113_I	117_V	1.607	1.00
43_Q	47_Y	1.606	1.00
7_L	76_F	1.604	1.00
8_G	49_A	1.597	1.00
89_L	98_G	1.568	1.00
38_W	41_G	1.510	1.00
11_N	76_F	1.506	1.00
47_Y	50_L	1.501	1.00
46_M	50_L	1.481	1.00
55_V	75_M	1.439	1.00
15_A	46_M	1.423	1.00
33_K	36_Q	1.356	1.00
8_G	12_A	1.338	0.99
30_I	35_L	1.308	0.99
77_A	107_A	1.289	0.99
9_A	116_V	1.268	0.99
6_I	120_V	1.239	0.99
7_L	11_N	1.234	0.99
70_T	73_W	1.230	0.99
116_V	120_V	1.228	0.99
36_Q	39_H	1.203	0.99
70_T	114_M	1.199	0.99
81_L	99_A	1.178	0.99
99_A	103_L	1.154	0.98
74_L	111_S	1.139	0.98
23_A	40_T	1.134	0.98
34_Y	90_S	1.128	0.98
34_Y	37_V	1.119	0.98
10_I	14_L	1.110	0.98
42_V	45_H	1.087	0.98
31_P	34_Y	1.074	0.98
48_H	108_F	1.068	0.97
48_H	112_W	1.046	0.97
37_V	89_L	1.044	0.97
97_L	100_I	1.043	0.97
8_G	56_A	1.040	0.97
50_L	54_V	1.016	0.97
67_S	118_A	1.015	0.97
22_G	45_H	0.997	0.96
103_L	107_A	0.990	0.96
33_K	37_V	0.979	0.96
38_W	43_Q	0.979	0.96
49_A	79_I	0.977	0.96
22_G	25_G	0.976	0.96
19_G	44_Y	0.975	0.96
10_I	116_V	0.961	0.95
6_I	119_A	0.948	0.95
85_S	89_L	0.934	0.95
106_V	110_I	0.930	0.94
9_A	115_I	0.928	0.94
16_V	48_H	0.899	0.93
51_G	111_S	0.884	0.93
25_G	30_I	0.873	0.92
88_I	92_T	0.855	0.91
38_W	45_H	0.850	0.91
89_L	99_A	0.845	0.91
81_L	103_L	0.839	0.91
67_S	117_V	0.834	0.90
15_A	47_Y	0.827	0.90
65_I	68_V	0.817	0.90
73_W	77_A	0.807	0.89
4_F	7_L	0.800	0.89
5_I	56_A	0.794	0.88
68_V	118_A	0.793	0.88
4_F	73_W	0.791	0.88
13_L	17_G	0.789	0.88
90_S	94_I	0.786	0.88
32_D	36_Q	0.784	0.88
26_L	91_V	0.778	0.87
110_I	114_M	0.775	0.87
21_F	25_G	0.760	0.86
29_K	66_G	0.750	0.85
41_G	84_G	0.737	0.84
71_A	118_A	0.734	0.84
26_L	38_W	0.733	0.84
55_V	68_V	0.732	0.84
12_A	46_M	0.729	0.83
48_H	79_I	0.727	0.83
13_L	116_V	0.724	0.83
11_N	79_I	0.720	0.83
5_I	119_A	0.707	0.82
59_A	68_V	0.704	0.81
15_A	49_A	0.698	0.81
8_G	54_V	0.696	0.81
71_A	115_I	0.667	0.78
21_F	86_L	0.666	0.78
88_I	99_A	0.665	0.77
14_L	18_L	0.663	0.77
38_W	42_V	0.656	0.77
3_V	29_K	0.653	0.76
55_V	72_G	0.644	0.75
34_Y	93_Q	0.643	0.75
37_V	90_S	0.637	0.74
89_L	101_T	0.633	0.74
52_L	72_G	0.629	0.73
36_Q	40_T	0.628	0.73
70_T	74_L	0.626	0.73
16_V	20_A	0.618	0.72
37_V	42_V	0.617	0.72
7_L	72_G	0.614	0.72
66_G	70_T	0.614	0.72
25_G	90_S	0.611	0.71
86_L	99_A	0.610	0.71
8_G	46_M	0.610	0.71
55_V	58_L	0.600	0.70
4_F	8_G	0.597	0.70
81_L	85_S	0.596	0.69
75_M	108_F	0.596	0.69
66_G	69_T	0.591	0.69
57_F	61_K	0.586	0.68
5_I	58_L	0.586	0.68
53_F	56_A	0.581	0.67
53_F	57_F	0.580	0.67
81_L	107_A	0.580	0.67
18_L	25_G	0.577	0.67
43_Q	115_I	0.575	0.67
41_G	90_S	0.574	0.67
54_V	57_F	0.572	0.66
38_W	50_L	0.571	0.66
81_L	100_I	0.564	0.65
11_N	15_A	0.564	0.65
42_V	46_M	0.563	0.65
86_L	92_T	0.561	0.65
67_S	70_T	0.561	0.65
85_S	100_I	0.560	0.65
12_A	47_Y	0.559	0.65
21_F	27_E	0.556	0.64
42_V	49_A	0.556	0.64
71_A	111_S	0.551	0.63
18_L	38_W	0.548	0.63
99_A	107_A	0.546	0.63
13_L	16_V	0.546	0.63
27_E	83_S	0.544	0.62
11_N	45_H	0.544	0.62
56_A	119_A	0.543	0.62
9_A	35_L	0.531	0.61
43_Q	46_M	0.525	0.60
58_L	115_I	0.518	0.59
15_A	45_H	0.518	0.59
101_T	106_V	0.517	0.59
69_T	113_I	0.511	0.58
73_W	76_F	0.509	0.57
36_Q	81_L	0.507	0.57
41_G	83_S	0.506	0.57
103_L	106_V	0.505	0.57
10_I	117_V	0.503	0.57
84_G	117_V	0.503	0.57
88_I	94_I	0.503	0.57
34_Y	95_S	0.502	0.56
52_L	83_S	0.501	0.56
15_A	42_V	0.500	0.56

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
3ayfA	2	0.9431	12.7	0.931	Contact Map
1v54A	1	0.9675	11.5	0.933	Contact Map
2gsmA	1	0.9268	7.2	0.938	Contact Map
2yevA	1	0.9675	6.9	0.939	Contact Map
3s8fA	1	0.9756	5.2	0.942	Contact Map
3mk7A	1	0.9756	5.2	0.942	Contact Map
3wfdB	1	0.9268	3.9	0.946	Contact Map
1fftA	1	0.9268	3.8	0.946	Contact Map
4i0uA	4	0.4797	1.6	0.956	Contact Map
4ev6A	3	0.4959	1.6	0.956	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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