YLBG - BACSU - GREMLIN Contacts

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YLBG - UPF0298 protein YlbG

UniProt:	O34658	Sequences: MENRRQGMVVYLHSLKQSKMLRKFGNVHYVSKRLKYVVLYCDMDQIEKTMDKIASYSFVKKVEPSYKPFLKLEFESKLDKAKEYDYKIGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	90 (79)
Sequences:	306 (229)
Seq/√Len:	25.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_Y	63_E	4.037	1.00
42_D	45_Q	3.200	1.00
27_V	37_V	2.892	1.00
9_V	38_V	2.839	1.00
50_M	64_P	2.698	0.99
66_Y	69_F	2.544	0.99
13_H	60_K	2.250	0.98
45_Q	48_K	2.216	0.97
6_Q	43_M	1.885	0.94
14_S	17_Q	1.732	0.90
8_M	46_I	1.629	0.87
24_F	56_Y	1.594	0.86
15_L	30_V	1.570	0.85
35_K	75_E	1.511	0.83
50_M	70_L	1.473	0.81
53_I	62_V	1.469	0.81
7_G	51_D	1.416	0.79
10_V	66_Y	1.393	0.77
8_M	50_M	1.373	0.76
48_K	51_D	1.336	0.74
78_L	81_A	1.261	0.70
37_V	67_K	1.246	0.69
22_R	27_V	1.238	0.68
6_Q	68_P	1.225	0.68
43_M	69_F	1.213	0.67
24_F	27_V	1.192	0.65
15_L	37_V	1.178	0.64
24_F	59_V	1.166	0.64
14_S	30_V	1.112	0.60
7_G	12_L	1.095	0.59
57_S	67_K	1.074	0.57
6_Q	9_V	1.015	0.53
76_S	79_D	1.009	0.52
16_K	26_N	0.997	0.52
20_M	58_F	0.988	0.51
12_L	37_V	0.987	0.51
46_I	50_M	0.982	0.50
9_V	56_Y	0.967	0.49
8_M	64_P	0.966	0.49
11_Y	23_K	0.960	0.49
30_V	55_S	0.958	0.49
11_Y	18_S	0.953	0.48
6_Q	69_F	0.952	0.48
33_R	54_A	0.952	0.48
7_G	80_K	0.944	0.48
78_L	82_K	0.918	0.46
24_F	33_R	0.917	0.46
44_D	47_E	0.912	0.45
30_V	70_L	0.912	0.45
41_C	49_T	0.890	0.44
15_L	20_M	0.888	0.44
30_V	33_R	0.883	0.43
53_I	58_F	0.880	0.43
29_Y	38_V	0.878	0.43
12_L	18_S	0.860	0.42
19_K	78_L	0.856	0.41
19_K	35_K	0.842	0.40
12_L	67_K	0.836	0.40
77_K	81_A	0.836	0.40
32_K	41_C	0.817	0.39
16_K	71_K	0.793	0.37
71_K	74_F	0.785	0.36
10_V	53_I	0.782	0.36
6_Q	35_K	0.764	0.35
42_D	50_M	0.759	0.35
53_I	56_Y	0.756	0.34
24_F	52_K	0.753	0.34
8_M	57_S	0.745	0.34
35_K	41_C	0.742	0.33
54_A	57_S	0.739	0.33
47_E	51_D	0.736	0.33
35_K	74_F	0.723	0.32
32_K	67_K	0.718	0.32
32_K	66_Y	0.716	0.32
13_H	17_Q	0.716	0.32
11_Y	57_S	0.710	0.31
71_K	75_E	0.707	0.31
20_M	75_E	0.703	0.31
13_H	74_F	0.695	0.30
10_V	54_A	0.693	0.30
52_K	68_P	0.682	0.30
16_K	54_A	0.680	0.29
76_S	82_K	0.661	0.28
27_V	41_C	0.658	0.28
76_S	81_A	0.657	0.28
23_K	52_K	0.648	0.28
15_L	18_S	0.644	0.27
16_K	38_V	0.641	0.27
8_M	62_V	0.640	0.27
32_K	52_K	0.635	0.27
8_M	35_K	0.629	0.26
63_E	66_Y	0.620	0.26
6_Q	74_F	0.619	0.26
23_K	73_E	0.617	0.26
12_L	53_I	0.612	0.26
14_S	22_R	0.608	0.25
7_G	73_E	0.605	0.25
12_L	15_L	0.604	0.25
15_L	19_K	0.595	0.25
4_R	43_M	0.594	0.25
61_K	70_L	0.585	0.24
75_E	78_L	0.580	0.24
50_M	54_A	0.571	0.23
41_C	46_I	0.567	0.23
79_D	82_K	0.565	0.23
55_S	77_K	0.562	0.23
72_L	78_L	0.562	0.23
14_S	72_L	0.559	0.23
32_K	75_E	0.549	0.22
11_Y	60_K	0.549	0.22
7_G	40_Y	0.545	0.22
18_S	78_L	0.540	0.22
20_M	67_K	0.532	0.21
44_D	77_K	0.516	0.21
36_Y	40_Y	0.514	0.20
58_F	61_K	0.508	0.20
71_K	80_K	0.501	0.20
23_K	63_E	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
3h11A	1	0.7	23.4	0.918	Contact Map
1u0sA	1	0.6556	10.7	0.93	Contact Map
3wiuA	2	0.9222	9.5	0.931	Contact Map
3whiA	2	0.9111	6.1	0.937	Contact Map
2p0oA	1	0.7778	5.5	0.938	Contact Map
3fslA	2	0.6111	5.4	0.938	Contact Map
4aqrD	1	0.6333	5.2	0.939	Contact Map
1jt8A	1	0.3444	5	0.939	Contact Map
2kviA	1	0.7222	5	0.939	Contact Map
2nzcA	3	0.7333	4.9	0.94	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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