Cyd_oper_YbgE - PFAM28P - GREMLIN Contacts

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Cyd_oper_YbgE - Cyd operon protein YbgE (Cyd_oper_YbgE)

PFAM:	PF09600	Sequences: LRALSLLLALALALLLTWYPALFADATGGADHGLLMLLMWAMSAGFVHGVGFVPRRWLWRWLFSPLAAWLLLLLGLLLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	79 (76)
Sequences:	817 (531)
Seq/√Len:	60.9
META:	0.624

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_W	63_F	5.481	1.00
10_L	14_L	3.800	1.00
5_S	48_H	3.605	1.00
35_L	39_M	2.621	1.00
45_G	72_L	2.372	1.00
33_G	36_M	2.065	1.00
9_A	45_G	1.876	1.00
44_A	68_A	1.809	1.00
56_R	59_W	1.770	0.99
47_V	63_F	1.574	0.99
52_F	55_R	1.573	0.99
13_A	46_F	1.565	0.99
19_Y	22_L	1.472	0.98
16_L	23_F	1.418	0.97
17_T	46_F	1.355	0.97
41_A	71_L	1.337	0.96
13_A	42_M	1.332	0.96
41_A	72_L	1.318	0.96
40_W	67_A	1.318	0.96
9_A	37_L	1.303	0.96
25_D	28_G	1.271	0.95
40_W	44_A	1.268	0.95
20_P	54_P	1.262	0.95
32_H	36_M	1.256	0.95
48_H	65_P	1.247	0.94
65_P	69_W	1.239	0.94
12_L	15_L	1.122	0.91
48_H	69_W	1.120	0.91
9_A	46_F	1.115	0.90
2_R	48_H	1.114	0.90
68_A	75_G	1.095	0.90
24_A	30_A	1.093	0.90
44_A	47_V	1.090	0.89
13_A	23_F	1.051	0.88
37_L	43_S	1.047	0.87
56_R	61_W	1.016	0.86
67_A	70_L	1.005	0.85
17_T	23_F	0.983	0.84
68_A	71_L	0.978	0.84
65_P	68_A	0.962	0.83
13_A	43_S	0.957	0.82
23_F	46_F	0.942	0.81
11_A	57_W	0.926	0.80
16_L	76_L	0.889	0.77
33_G	72_L	0.884	0.77
45_G	68_A	0.879	0.76
16_L	39_M	0.878	0.76
8_L	73_L	0.870	0.76
13_A	16_L	0.862	0.75
10_L	13_A	0.856	0.75
32_H	60_R	0.836	0.73
14_L	37_L	0.836	0.73
6_L	45_G	0.822	0.72
2_R	5_S	0.818	0.71
11_A	76_L	0.811	0.70
7_L	11_A	0.810	0.70
18_W	43_S	0.808	0.70
3_A	7_L	0.802	0.70
35_L	41_A	0.801	0.70
41_A	75_G	0.791	0.69
8_L	69_W	0.780	0.67
47_V	64_S	0.775	0.67
13_A	35_L	0.775	0.67
14_L	18_W	0.760	0.65
7_L	77_L	0.759	0.65
54_P	60_R	0.749	0.64
53_V	56_R	0.742	0.64
13_A	65_P	0.720	0.61
10_L	38_L	0.720	0.61
12_L	42_M	0.693	0.58
38_L	49_G	0.693	0.58
6_L	47_V	0.687	0.58
33_G	43_S	0.687	0.58
11_A	14_L	0.684	0.57
5_S	69_W	0.684	0.57
20_P	43_S	0.679	0.57
24_A	27_T	0.674	0.56
39_M	52_F	0.662	0.55
25_D	29_G	0.661	0.55
4_L	40_W	0.654	0.54
39_M	43_S	0.650	0.54
12_L	38_L	0.649	0.53
58_L	76_L	0.643	0.53
74_L	77_L	0.642	0.53
26_A	70_L	0.639	0.52
6_L	14_L	0.633	0.52
16_L	21_A	0.629	0.51
13_A	17_T	0.624	0.51
20_P	32_H	0.621	0.50
26_A	29_G	0.613	0.49
34_L	66_L	0.607	0.49
40_W	61_W	0.593	0.47
40_W	71_L	0.581	0.46
58_L	61_W	0.579	0.46
9_A	68_A	0.578	0.45
7_L	30_A	0.577	0.45
30_A	38_L	0.574	0.45
28_G	52_F	0.566	0.44
60_R	67_A	0.560	0.43
6_L	49_G	0.546	0.42
45_G	54_P	0.540	0.41
19_Y	59_W	0.538	0.41
21_A	26_A	0.537	0.41
32_H	43_S	0.527	0.40
47_V	59_W	0.526	0.40
54_P	63_F	0.524	0.39
12_L	36_M	0.524	0.39
44_A	73_L	0.518	0.39
40_W	63_F	0.516	0.39
5_S	9_A	0.509	0.38
3_A	8_L	0.507	0.38
7_L	25_D	0.506	0.38
15_L	39_M	0.503	0.37
28_G	40_W	0.500	0.37

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
4ryoA	1	0.962	12.4	0.882	Contact Map
2mgyA	1	0.962	9.7	0.888	Contact Map
4uc1A	3	0.962	3.7	0.908	Contact Map
4g9iA	1	0.5443	2.2	0.918	Contact Map
3tx3A	2	0.519	2	0.92	Contact Map
1m0kA	3	0.5823	2	0.92	Contact Map
4p02A	1	0.8734	1.9	0.921	Contact Map
2qtsA	4	0.2405	1.6	0.924	Contact Map
4xp4A	1	0.9747	1.6	0.924	Contact Map
3wajA	1	1	1.4	0.927	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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