DUF3339 - PFAM28P - GREMLIN Contacts

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DUF3339 - Protein of unknown function (DUF3339)

PFAM:	PF11820	Sequences: MADWGPVLVAVVLFVLLSPGLLLQLPGKSRGVEFGNMQTSGASILVHALVFFLLFAILLLAIGVHIY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (65)
Sequences:	632 (300)
Seq/√Len:	37.2
META:	0.481

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_S	43_S	4.859	1.00
8_L	66_I	4.069	1.00
24_Q	43_S	3.308	1.00
29_S	38_Q	3.021	1.00
10_A	55_F	2.657	1.00
24_Q	40_S	2.015	0.99
54_L	58_L	2.003	0.99
50_V	54_L	1.765	0.97
31_G	38_Q	1.557	0.94
12_V	36_N	1.537	0.93
5_G	11_V	1.449	0.91
27_G	32_V	1.399	0.89
12_V	16_L	1.359	0.88
7_V	11_V	1.342	0.87
24_Q	36_N	1.309	0.86
51_F	59_L	1.246	0.83
13_L	17_L	1.238	0.82
21_L	44_I	1.225	0.82
25_L	53_L	1.205	0.81
27_G	33_E	1.195	0.80
2_A	29_S	1.164	0.78
23_L	48_A	1.161	0.78
5_G	10_A	1.152	0.77
55_F	59_L	1.148	0.77
10_A	42_A	1.119	0.75
21_L	43_S	1.116	0.75
21_L	24_Q	1.090	0.73
28_K	58_L	1.053	0.71
41_G	57_I	1.012	0.68
11_V	65_H	1.007	0.67
11_V	15_V	1.002	0.67
16_L	53_L	0.981	0.65
39_T	44_I	0.978	0.65
15_V	33_E	0.973	0.65
28_K	38_Q	0.971	0.64
37_M	56_A	0.968	0.64
52_F	56_A	0.956	0.63
24_Q	37_M	0.945	0.62
3_D	6_P	0.922	0.60
48_A	66_I	0.909	0.59
18_S	63_G	0.908	0.59
32_V	45_L	0.884	0.57
6_P	10_A	0.871	0.56
24_Q	30_R	0.860	0.55
9_V	49_L	0.851	0.54
38_Q	53_L	0.802	0.50
56_A	66_I	0.797	0.49
10_A	50_V	0.785	0.48
41_G	52_F	0.781	0.48
12_V	15_V	0.779	0.48
5_G	63_G	0.771	0.47
52_F	61_A	0.770	0.47
15_V	37_M	0.728	0.43
51_F	55_F	0.725	0.43
22_L	46_V	0.725	0.43
17_L	48_A	0.713	0.42
12_V	26_P	0.709	0.42
16_L	54_L	0.681	0.39
49_L	62_I	0.673	0.39
5_G	13_L	0.673	0.39
4_W	50_V	0.667	0.38
11_V	22_L	0.666	0.38
18_S	45_L	0.663	0.38
30_R	33_E	0.660	0.38
22_L	48_A	0.657	0.37
7_V	53_L	0.649	0.37
25_L	57_I	0.649	0.37
18_S	39_T	0.640	0.36
43_S	57_I	0.633	0.35
13_L	32_V	0.622	0.35
14_F	17_L	0.618	0.34
26_P	36_N	0.604	0.33
2_A	63_G	0.600	0.33
30_R	34_F	0.595	0.32
26_P	60_L	0.595	0.32
45_L	66_I	0.594	0.32
23_L	37_M	0.590	0.32
25_L	46_V	0.587	0.32
10_A	56_A	0.586	0.32
14_F	20_G	0.586	0.32
9_V	27_G	0.579	0.31
63_G	66_I	0.576	0.31
42_A	48_A	0.572	0.31
11_V	28_K	0.572	0.31
36_N	56_A	0.565	0.30
24_Q	38_Q	0.558	0.30
21_L	30_R	0.554	0.29
2_A	53_L	0.552	0.29
22_L	54_L	0.530	0.28
16_L	62_I	0.523	0.27
31_G	37_M	0.520	0.27
22_L	28_K	0.518	0.27
24_Q	28_K	0.512	0.26
38_Q	61_A	0.512	0.26
58_L	64_V	0.511	0.26
10_A	49_L	0.508	0.26
7_V	10_A	0.504	0.26
7_V	41_G	0.500	0.26

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
4hygA	3	0.9104	3.2	0.912	Contact Map
1kqfC	3	0.8955	3.1	0.913	Contact Map
3i94A	1	0.5821	1.8	0.923	Contact Map
2l9uA	2	0.4328	1.6	0.926	Contact Map
4huqT	1	0.2836	1.2	0.931	Contact Map
4ltoA	3	0.3731	1.2	0.932	Contact Map
3wu2Z	1	0.3731	1.1	0.932	Contact Map
2m0jB	1	0.1493	1.1	0.934	Contact Map
4cbcA	3	0.3582	0.9	0.937	Contact Map
3rceA	1	0.4328	0.9	0.937	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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