DUF3888 - PFAM28P - GREMLIN Contacts

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DUF3888 - Protein of unknown function (DUF3888)

PFAM:	PF13027	Sequences: YQDALLTLLLPYIQKAINNYYGEYLTYSPWDVEILSIKRVNGFRGFDFEVTVEVTPFVGPHNPPVGKDTITFEISPGGVKLIKFEHLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (85)
Sequences:	539 (444)
Seq/√Len:	48.2
META:	0.56

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_E	67_K	3.090	1.00
72_F	81_L	3.061	1.00
3_D	39_R	2.850	1.00
66_G	86_H	2.810	1.00
16_A	19_N	2.572	1.00
39_R	48_F	2.452	1.00
68_D	86_H	2.452	1.00
56_P	65_V	2.409	1.00
70_I	81_L	2.176	1.00
25_L	65_V	1.820	0.99
53_E	69_T	1.783	0.99
25_L	58_V	1.731	0.98
13_I	54_V	1.706	0.98
3_D	48_F	1.690	0.98
28_S	57_F	1.670	0.98
67_K	87_L	1.629	0.98
56_P	64_P	1.591	0.97
9_L	74_I	1.469	0.96
21_Y	66_G	1.411	0.95
56_P	69_T	1.403	0.94
38_K	49_E	1.367	0.94
50_V	72_F	1.323	0.92
5_L	8_L	1.317	0.92
13_I	70_I	1.297	0.92
58_V	65_V	1.273	0.91
73_E	80_K	1.259	0.90
15_K	19_N	1.236	0.90
35_L	69_T	1.229	0.89
57_F	62_N	1.187	0.88
39_R	46_F	1.185	0.88
54_V	68_D	1.169	0.87
33_E	53_E	1.169	0.87
56_P	66_G	1.154	0.86
4_A	45_G	1.087	0.83
21_Y	86_H	1.085	0.82
17_I	80_K	1.078	0.82
56_P	68_D	1.060	0.81
17_I	54_V	1.054	0.81
50_V	74_I	1.039	0.80
52_V	74_I	1.033	0.79
28_S	31_D	1.026	0.79
7_T	82_I	1.011	0.78
74_I	79_V	1.002	0.77
40_V	45_G	0.979	0.75
49_E	73_E	0.976	0.75
73_E	82_I	0.955	0.74
51_T	69_T	0.944	0.73
77_G	85_E	0.940	0.72
59_G	62_N	0.922	0.71
16_A	81_L	0.919	0.71
56_P	87_L	0.916	0.70
33_E	37_I	0.910	0.70
56_P	61_H	0.909	0.70
69_T	87_L	0.905	0.70
25_L	56_P	0.892	0.68
21_Y	68_D	0.883	0.68
16_A	84_F	0.863	0.66
68_D	72_F	0.863	0.66
29_P	33_E	0.862	0.66
48_F	55_T	0.848	0.64
70_I	83_K	0.844	0.64
67_K	72_F	0.835	0.63
22_G	27_Y	0.825	0.62
20_Y	86_H	0.823	0.62
20_Y	66_G	0.823	0.62
67_K	73_E	0.819	0.62
9_L	79_V	0.817	0.62
15_K	18_N	0.817	0.62
59_G	65_V	0.809	0.61
29_P	32_V	0.795	0.59
64_P	87_L	0.794	0.59
36_S	51_T	0.791	0.59
43_F	87_L	0.778	0.58
52_V	55_T	0.764	0.56
9_L	52_V	0.759	0.56
51_T	85_E	0.754	0.55
66_G	84_F	0.753	0.55
68_D	87_L	0.751	0.55
47_D	73_E	0.739	0.54
41_N	83_K	0.737	0.54
27_Y	36_S	0.732	0.53
9_L	48_F	0.714	0.51
41_N	45_G	0.692	0.49
35_L	53_E	0.680	0.48
53_E	80_K	0.680	0.48
34_I	73_E	0.674	0.47
12_Y	79_V	0.661	0.46
43_F	46_F	0.659	0.46
18_N	34_I	0.656	0.46
3_D	11_P	0.649	0.45
37_I	77_G	0.648	0.45
51_T	74_I	0.646	0.45
64_P	72_F	0.643	0.44
61_H	66_G	0.642	0.44
11_P	60_P	0.642	0.44
3_D	42_G	0.629	0.43
36_S	47_D	0.621	0.42
53_E	71_T	0.612	0.41
18_N	57_F	0.609	0.41
26_T	57_F	0.607	0.41
32_V	37_I	0.607	0.41
20_Y	24_Y	0.587	0.39
65_V	68_D	0.585	0.39
42_G	45_G	0.585	0.39
43_F	57_F	0.583	0.38
22_G	36_S	0.573	0.37
20_Y	23_E	0.573	0.37
15_K	82_I	0.572	0.37
40_V	47_D	0.570	0.37
72_F	79_V	0.570	0.37
35_L	87_L	0.566	0.37
19_N	83_K	0.542	0.35
31_D	57_F	0.539	0.34
12_Y	38_K	0.530	0.34
80_K	85_E	0.530	0.34
24_Y	38_K	0.524	0.33
47_D	75_S	0.523	0.33
67_K	76_P	0.522	0.33
35_L	41_N	0.521	0.33
5_L	73_E	0.519	0.33
31_D	55_T	0.517	0.32
40_V	54_V	0.512	0.32
78_G	82_I	0.510	0.32
2_Q	60_P	0.508	0.32
7_T	74_I	0.505	0.31
5_L	43_F	0.503	0.31
41_N	80_K	0.501	0.31
38_K	84_F	0.500	0.31

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
2d3o1	1	0.5341	34.5	0.872	Contact Map
2nscA	2	0.5341	24.5	0.881	Contact Map
1p9yA	1	0.625	16.5	0.89	Contact Map
1t11A	3	0.875	15.5	0.891	Contact Map
1w26A	1	0.9091	15.5	0.891	Contact Map
2rsxA	1	0.9205	10.2	0.9	Contact Map
4gl6A	1	0.8636	5.3	0.912	Contact Map
4ioyX	1	0.7273	4.5	0.915	Contact Map
3a9lA	2	0.2727	3.7	0.919	Contact Map
4yjwA	1	0.25	3.1	0.922	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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