DUF3717 - PFAM28P - GREMLIN Contacts

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DUF3717 - Protein of unknown function (DUF3717)

PFAM:	PF12512	Sequences: GIHITDIEAAINYWRERSPSPDEGITLCPEVRALAEVYALMVYYREDEADEASLPAAARAAWLAWYD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (65)
Sequences:	1459 (681)
Seq/√Len:	84.4
META:	0.881

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_C	31_V	3.229	1.00
18_S	30_E	2.843	1.00
13_Y	27_L	2.733	1.00
30_E	64_A	2.540	1.00
40_L	44_Y	2.321	1.00
27_L	31_V	2.157	1.00
22_D	25_I	2.091	1.00
54_L	59_R	1.855	1.00
2_I	62_W	1.849	1.00
59_R	63_L	1.766	1.00
60_A	64_A	1.748	1.00
49_A	54_L	1.585	1.00
62_W	66_Y	1.546	1.00
3_H	6_D	1.526	1.00
18_S	28_C	1.422	0.99
1_G	48_E	1.409	0.99
8_E	12_N	1.406	0.99
12_N	38_Y	1.387	0.99
1_G	7_I	1.387	0.99
12_N	15_R	1.355	0.99
21_P	25_I	1.355	0.99
13_Y	17_R	1.302	0.98
8_E	11_I	1.297	0.98
17_R	40_L	1.167	0.97
46_E	49_A	1.110	0.96
8_E	38_Y	1.092	0.95
63_L	66_Y	1.074	0.95
11_I	38_Y	1.066	0.95
46_E	53_S	1.044	0.94
17_R	57_A	1.019	0.93
33_A	58_A	0.998	0.93
55_P	58_A	0.994	0.93
3_H	42_V	0.973	0.92
28_C	32_R	0.970	0.92
21_P	24_G	0.962	0.91
44_Y	53_S	0.928	0.90
20_S	24_G	0.917	0.89
8_E	15_R	0.913	0.89
49_A	53_S	0.905	0.89
50_D	53_S	0.905	0.89
47_D	56_A	0.897	0.88
33_A	37_V	0.891	0.88
41_M	49_A	0.889	0.88
52_A	59_R	0.889	0.88
35_A	65_W	0.883	0.87
4_I	42_V	0.866	0.86
37_V	55_P	0.843	0.85
25_I	32_R	0.838	0.84
6_D	66_Y	0.838	0.84
56_A	59_R	0.830	0.84
20_S	38_Y	0.792	0.81
13_Y	49_A	0.791	0.81
13_Y	64_A	0.775	0.80
37_V	40_L	0.765	0.79
47_D	63_L	0.742	0.77
33_A	61_A	0.742	0.77
22_D	32_R	0.733	0.76
14_W	38_Y	0.731	0.75
12_N	27_L	0.725	0.75
44_Y	57_A	0.724	0.75
5_T	65_W	0.724	0.75
54_L	57_A	0.718	0.74
18_S	32_R	0.713	0.74
1_G	6_D	0.712	0.74
25_I	28_C	0.704	0.73
16_E	46_E	0.699	0.72
49_A	52_A	0.693	0.72
3_H	66_Y	0.675	0.70
35_A	45_R	0.671	0.69
14_W	33_A	0.669	0.69
52_A	57_A	0.649	0.67
1_G	49_A	0.645	0.66
15_R	38_Y	0.628	0.64
14_W	30_E	0.619	0.63
58_A	61_A	0.612	0.62
7_I	49_A	0.605	0.61
21_P	28_C	0.588	0.59
39_A	43_Y	0.587	0.59
11_I	15_R	0.577	0.58
9_A	62_W	0.573	0.57
36_E	40_L	0.568	0.56
41_M	44_Y	0.567	0.56
1_G	53_S	0.566	0.56
2_I	27_L	0.552	0.54
19_P	30_E	0.551	0.54
1_G	50_D	0.539	0.53
8_E	42_V	0.536	0.52
13_Y	31_V	0.536	0.52
56_A	63_L	0.534	0.52
48_E	51_E	0.530	0.51
37_V	43_Y	0.529	0.51
58_A	62_W	0.528	0.51
31_V	35_A	0.527	0.51
49_A	57_A	0.518	0.50
22_D	26_T	0.516	0.49
44_Y	56_A	0.510	0.49
47_D	57_A	0.502	0.48
14_W	34_L	0.500	0.47

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
4lvcA	4	0.9254	23.1	0.868	Contact Map
4p29A	1	0.5224	12.9	0.882	Contact Map
2mhkA	1	0.6269	12.2	0.883	Contact Map
1v8bA	4	0.9254	10.2	0.887	Contact Map
3d64A	4	0.9254	9.9	0.888	Contact Map
3x2fA	4	0.9403	7.6	0.894	Contact Map
2marA	1	0.8657	6.4	0.897	Contact Map
2knzA	1	0.2985	5.8	0.899	Contact Map
2xsdC	1	0.9701	5.5	0.9	Contact Map
4k70A	2	0.8657	4.8	0.903	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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